cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14801757
title: Frei Recordings (DEC, JAN, FEB)

description: This repository contains audio recordings from the 2022-2023 Antarctic Summer Campaign corresponding to the project "Evaluation of the soundscape composition and antropoghenic noise impact at Ardley Island (Maxwell Bay) and Fildes Peninsula (King George/South Shetland island)" from Universidad de la República (Montevideo, Uruguay). In this case the recordings correspond to Frei (S62°12'07.3" W58°57'55.7") monitoring point. 

 

Recordings where made using Audiomoth recorders. Each file consists of a 5 minutes recording made at 48kHz with a Med-High gain. The recordings where made periodically during the first five minutes of every hour, for 24 hours during all days of the summer campaign. The folders in this repository are divided by month, which inside contains folder indicating date of recording, and the name of the file indicate hour (in GMT time) as: YYYYMMDD_HH
DOI: 10.5281/zenodo.10666413
title: Geometric deep learning improves generalizability of MHC-bound peptide predictions

description: Full dataset and trained models from the manuscript "Geometric deep learning improves generalizability of MHC-bound peptide predictions".

"outputs_and-BA_data.zip" contains the networks' outputs for each cross-validation experiment and a "full_dataset.csv" containing the initial BA data.Note: this file has been updated (2024/11/26) due to errors in generating some of the previous csvs. In the earlier version, both MLP and CNN outputs reported were wrong. The correct values are now reported in the updated csvs.

"trained_models.zip" contains all the trained models parameters

"propedia_ssl.zip" contains all the 3D models from propedia used to train the 3D-SSL

"pdb.zip" contains 3D models generated in PANDORA and used to train CNN, GNN and EGNN. It amounts to 145665 .pdb files, one for each human binding affinity entry from the initial dataset from O'Donnell et al. The list of entries used to actually train networks after filtering can be found in outputs_and-BA_data.zip", in the "full_dataset.csv" file. 

 

CHANGELOG v4:

- In outputs_and-BA-data.zip, updated CNN_AlleleClustered_test_crossval.csv and CNN_shuffled_test_crossval.csv. These file had the wrong IDs paired with the network outputs.The IDs and labels are now consistent with the outputs.

- Updated reference from the preprint to the published article.
DOI: 10.5281/zenodo.10666414
title: Geometric deep learning improves generalizability of MHC-bound peptide predictions

description: Full dataset and trained models from the manuscript "Geometric deep learning improves generalizability of MHC-bound peptide predictions".

"outputs_and-BA_data.zip" contains the networks' outputs for each cross-validation experiment and a "full_dataset.csv" containing the initial BA data.

"trained_models.zip" contains all the trained models parameters

"propedia_ssl.zip" contains all the 3D models from propedia used to train the 3D-SSL

"pdb.zip" will be uploaded soon, containing all the 3D models generated in PANDORA and used to train CNN, GNN and EGNN.
DOI: 10.5281/zenodo.13759345
title: Geometric deep learning improves generalizability of MHC-bound peptide predictions

description: Full dataset and trained models from the manuscript "Geometric deep learning improves generalizability of MHC-bound peptide predictions".

"outputs_and-BA_data.zip" contains the networks' outputs for each cross-validation experiment and a "full_dataset.csv" containing the initial BA data.

"trained_models.zip" contains all the trained models parameters

"propedia_ssl.zip" contains all the 3D models from propedia used to train the 3D-SSL

"pdb.zip" contains 3D models generated in PANDORA and used to train CNN, GNN and EGNN. It amounts to 145665 .pdb files, one for each human binding affinity entry from the initial dataset from O'Donnell et al. The list of entries used to actually train networks after filtering can be found in outputs_and-BA_data.zip", in the "full_dataset.csv" file.
DOI: 10.5281/zenodo.14223679
title: Geometric deep learning improves generalizability of MHC-bound peptide predictions

description: Full dataset and trained models from the manuscript "Geometric deep learning improves generalizability of MHC-bound peptide predictions".

"outputs_and-BA_data.zip" contains the networks' outputs for each cross-validation experiment and a "full_dataset.csv" containing the initial BA data.Note: this file has been updated (2024/11/26) due to errors in generating some of the previous csvs. In the earlier version, both MLP and CNN outputs reported were wrong. The correct values are now reported in the updated csvs.

"trained_models.zip" contains all the trained models parameters

"propedia_ssl.zip" contains all the 3D models from propedia used to train the 3D-SSL

"pdb.zip" contains 3D models generated in PANDORA and used to train CNN, GNN and EGNN. It amounts to 145665 .pdb files, one for each human binding affinity entry from the initial dataset from O'Donnell et al. The list of entries used to actually train networks after filtering can be found in outputs_and-BA_data.zip", in the "full_dataset.csv" file.
DOI: 10.5281/zenodo.14906231
title: Geometric deep learning improves generalizability of MHC-bound peptide predictions

description: Full dataset and trained models from the manuscript "Geometric deep learning improves generalizability of MHC-bound peptide predictions".

"outputs_and-BA_data.zip" contains the networks' outputs for each cross-validation experiment and a "full_dataset.csv" containing the initial BA data.Note: this file has been updated (2024/11/26) due to errors in generating some of the previous csvs. In the earlier version, both MLP and CNN outputs reported were wrong. The correct values are now reported in the updated csvs.

"trained_models.zip" contains all the trained models parameters

"propedia_ssl.zip" contains all the 3D models from propedia used to train the 3D-SSL

"pdb.zip" contains 3D models generated in PANDORA and used to train CNN, GNN and EGNN. It amounts to 145665 .pdb files, one for each human binding affinity entry from the initial dataset from O'Donnell et al. The list of entries used to actually train networks after filtering can be found in outputs_and-BA_data.zip", in the "full_dataset.csv" file. 

 

CHANGELOG v4:

- In outputs_and-BA-data.zip, updated CNN_AlleleClustered_test_crossval.csv and CNN_shuffled_test_crossval.csv. These file had the wrong IDs paired with the network outputs.The IDs and labels are now consistent with the outputs.

- Updated reference from the preprint to the published article.
DOI: 10.25921/3t9f-4618
title: Partial pressure (or fugacity) of carbon dioxide, water temperature, salinity and other variables collected from surface underway observations from R/V Oden Arctic Ocean 2018 cruise (EXPOCODE 77DN20180818) in the Arctic Ocean from 2018-08-18 to 2018-09-09 (NCEI Accession 0292108)

description: This dataset includes surface underway, chemical, meteorological and physical data collected from R/V Oden Arctic Ocean 2018 cruise (EXPOCODE 77DN20180818) in the Arctic Ocean from 2018-08-18 to 2018-09-09. These data include water temperature, barometric pressure, partial pressure (or fugacity) of carbon dioxide - atmosphere, partial pressure (or fugacity) of carbon dioxide - water. Research expedition to central Arctic Ocean onboard Icebreaker Oden. During an ice camp close to the North Pole, The pCO2 system was deployed from a temporary mooring in a lead adjacent to the ice floe to which Oden was moored, approximately 1.5 km from Oden's position. The sensor was positioned approx 2 m from the ice edge and drew water through a pumped intake at 0.5 m depth.
DOI: 10.25921/bhvm-2v34
title: Partial pressure (or fugacity) of carbon dioxide, water temperature, salinity and other variables collected from surface underway observations from R/V Oden Synoptic Arctic Survey 2021 cruise (EXPOCODE 77DN20210802) in the Arctic Ocean from 2021-08-02 to 2021-09-11 (NCEI Accession 0292109)

description: This dataset includes surface underway, chemical, meteorological and physical data collected from R/V Oden Synoptic Arctic Survey 2021 cruise (EXPOCODE 77DN20210802) in the Arctic Ocean from 2021-08-02 to 2021-09-11. These data include water temperature, barometric pressure, partial pressure (or fugacity) of carbon dioxide - atmosphere, partial pressure (or fugacity) of carbon dioxide - water. Research expedition to central Arctic Ocean onboard Icebreaker Oden. https://www.polar.se/en/expeditions/previous-expeditions/arctic/synoptic-arctic-survey-2021/. During an ice camp close to the North Pole, The pCO2 system was deployed from a temporary mooring in a lead adjacent to the ice floe to which Oden was moored, approximately 1.5 km from Oden's position. The sensor was positioned approx 2 m from the ice edge and drew water through a pumped intake at 0.5 m depth. Abstract
DOI: 10.5281/zenodo.14780840
title: Ardley Recordings (DEC, JAN, FEB)

description: This repository contains audio recordings from the 2022-2023 Antarctic Summer Campaign corresponding to the project "Evaluation of the soundscape composition and antropoghenic noise impact at Ardley Island (Maxwell Bay) and Fildes Peninsula (King George/South Shetland island)" from Universidad de la República (Montevideo, Uruguay). In this case the recordings correspond to Ardley Island (S62°12'36.3" W58°55'33.2") monitoring point. 

 

Recordings where made using Audiomoth recorders. Each file consists of a 5 minutes recording made at 48kHz with a Med-High gain. The recordings where made periodically during the first five minutes of every hour, for 24 hours during all days of the summer campaign. The folders in this repository are divided by month, which inside contains folder indicating date of recording, and the name of the file indicate hour (in GMT time) as: YYYYMMDD_HH
DOI: 10.25921/d0cm-qk72
title: Partial pressure of carbon dioxide, temperature, salinity and other variables collected from the coastal surface underway observations from NOAA Ship Gordon Gunter in the Gulf of Mexico and Atlantic Ocean in 2024 (NCEI Accession 0292653)

description: This dataset includes surface underway measurements of mole fraction of CO2 in the equilibrator headspace (dry) at equilibrator temperature, mole fraction of CO2 measured in dry outside air, barometric pressure in the equilibrator headspace, barometric pressure, corrected to sea level, water temperature in equilibrator, sea surface temperature, sea surface salinity, fugacity of CO2 in sea water at SST and 100% humidity, and difference between sea water fCO2 and interpolated air fCO2 measured during the NOAA Ship Gordon Gunter cruises in the Gulf of Mexico and Atlantic Ocean in 2024. The instruments used to collect these data include carbon dioxide (CO2) gas analyzer and shower head chamber equilibrator for autonomous carbon dioxide (CO2) measurement.
DOI: 10.25921/kg4y-7622
title: Partial pressure of carbon dioxide, water temperature, salinity and other variables collected from surface underway observations during Ships of Opportunity (SOOP) M/V Le Commandant Charcot cruise lines in the North Atlantic Ocean, South Atlantic Ocean, South Pacific Ocean, North Pacific Ocean, Southern Ocean, Arctic Ocean in 2023 (NCEI Accession 0292658)

description: This dataset consists of the surface underway measurements of mole fraction of CO2 in the equilibrator headspace (dry) at equilibrator temperature (ppm), mole fraction of CO2 measured in dry outside air (ppm), mole fraction of CO2 in outside air associated with each water analysis. These values are interpolated between the bracketing averaged good xCO2_ATM analyses (ppm), barometric pressure in the equilibrator headspace (hPa), barometric pressure measured outside, corrected to sea level (hPa), water temperature in equilibrator (°C), sea surface temperature (°C), sea surface salinity, fugacity of CO2 in sea water at SST and 100% humidity (μatm), fugacity of CO2 in air corresponding to the interpolated xCO2 at SST and 100% humidity (μatm), sea water fCO2 minus interpolated air fCO2 (μatm). The measurement were performed during the SOOP M/V Le Commandant Charcot cruises in the North Atlantic Ocean, South Atlantic Ocean, South Pacific Ocean, North Pacific Ocean, Southern Ocean, Arctic Ocean in 2023.
DOI: 10.25921/e0qf-7553
title: Partial pressure of carbon dioxide, temperature, salinity and other variables collected from the coastal surface underway observations from NOAA Ship Henry B. Bigelow in the North Atlantic Ocean, US North-East Coast in 2024 (NCEI Accession 0292724)

description: This dataset includes surface underway, chemical, meteorological and physical data collected from NOAA Ship Henry B. Bigelow in the North Atlantic Ocean, US North East Coast in 2024. These data include measurements of mole fraction of carbon dioxide (CO2) in the equilibrator headspace (dry) at equilibrator temperature, mole fraction of CO2 measured in dry outside air, barometric pressure in the equilibrator headspace, barometric pressure, corrected to sea level, water temperature in equilibrator, sea surface temperature, sea surface salinity, fugacity of CO2 in sea water at SST and 100% humidity, and difference between sea water fugacity of CO2 (fCO2) and interpolated air fCO2. The instruments used to collect these data include carbon dioxide gas analyzer and shower head chamber equilibrator for autonomous carbon dioxide measurement. In February 2011, the Ocean Carbon Group at NOAA's Atlantic Oceanographic and Meteorological Laboratory (AOML) installed an instrument to measure CO2 levels in surface water and air on NOAA Ship Henry B. Bigelow. The Bigelow primarily operates in the North Atlantic Ocean between North Carolina and Maine.
DOI: 10.25921/jrj7-aq38
title: Stable oxygen isotopes, water temperature, salinity, and others taken by CTD and water samples from the research vessel Thomas G. Thompson in the South Indian Ocean from 2018-11-07 to 2018-12-12 (NCEI Accession 0292785)

description: This dataset contains water temperature, salinity, and oxygen concentration taken by CTD, as well as stable oxygen and hydrogen isotope observations inferred from laboratory analyses of seawater samples during cruise TN362 aboard the R/V Thomas G. Thompson in the South Indian Ocean. Data are in XLSX format.
DOI: 10.25921/71ay-f182
title: Survey of marsh soil and vegetation properties in Barataria Basin (Louisiana, USA) from 2018-05-09 to 2023-07-27 (NCEI Accession 0292959)

description: A survey of marsh plants and soil properties was conducted in Barataria Basin (Louisiana, USA), between 2018 and 2023. A total of 74 sites were surveyed across four different salinity zones (fresh, intermediate, brackish, saline). At most sites, measurements were taken at the edge (1-3m from the actual marsh edge with the open water), and in the interior (20-25 m from the edge). At each site (both edge and interior), ten vertical profiles (every 10 cm, up to 55 cm depth) of soil strength were collected. Marsh strength was measured with a Humboldt “field vane shear set” (vane size 25.4 x 50.7mm). Marsh elevation was measured with an RTK GPS. Plant type was determined by visual inspection, according to the Daubenmire cover-class method. Soil dry bulk density and organic content was measured in the lab, based on one core taken at each site (both edge and interior).

An excel spreadsheet is included with tabs representing data from each experiment or sample type with a README tab with more information on each. Missing values are where a measurement was not taken and should be treated as NaN.
DOI: 10.25921/f0jw-ja07
title: GIS land management and development layers to support the management of juvenile habitats in Charlotte County, Florida from 2021-09-01 to 2021-12-30 (NCEI Accession 0293502)

description: The data included are geographic information layers relevant to sportfish ecology, land development, community planning, zoning, coastal zone management, storm water management, future land use, land ownership, and planning tools and techniques aggregated from other sources during the project titled "Knowledge Co-Production for Place-Based Recreational Fishery Conservation in Charlotte Harbor, Florida". Data contributors assume no liability for any errors, omissions, or inaccuracies in the information provided regardless of how caused. The layers are each provided as separate KMZ files.
DOI: 10.5284/1126684
title: Data from a Trial Trenching at Dalehouse Lane, Kenilworth, Warwickshire, 2017-2023 (HS2 Phase One)

description: This collection comprises of reports, images, spreadsheets, databases, GIS data and site records from an archaeological trial trenching carried out at Dalehouse Lane, Kenilworth, Warwickshire by Connect Archaeology between 29th May and 5th June 2017.
DOI: 10.25921/b6bm-bc04
title: Water temperature, salinity, and others collected by CTD from the passenger ship LE COMMANDANT CHARCOT in Northwestern Passages, Northwest Atlantic Ocean (limit-40 W), and North Pacific Ocean from 2023-09-12 to 2023-10-09 (NCEI Accession 0294335)

description: This dataset contains water temperature, salinity, and others collected by CTD from LE COMMANDANT CHARCOT in Northwestern Passages, Northwest Atlantic Ocean, and North Pacific Ocean. Due to global warming, the Arctic is experiencing rising temperatures resulting in the thawing of permafrost soil and an increase of glacial mass loss. These processes are expected to increase the flux of inorganic and organic nutrients into coastal ecosystems, reduce the salinity of surface waters, and change light conditions of the water column. Together, these environmental changes can affect the composition and distribution of the plankton community, likely favoring harmful algal species and associated phycotoxins. These harmful algae can impact public health and the economy of areas dependent on arctic resources. The aim of this project is to establish a baseline of the phytoplankton community composition in two understudied Arctic systems, heavily impacted by global warming: fjord systems with melting glaciers and coastal ecosystems impacted by permafrost thawing. To that end, oceanographic parameters (e.g., dissolved nutrients and organic carbon) and vitamins that shape the phytoplankton community, as well as dissolved and particulate phycotoxins, will be measured. Particulate phycotoxins will be studied both at the producer level (phytoplankton) and at the zooplankton level (phytoplankton natural predators), to address transference and conversion of phycotoxins in the first levels of the trophic web. Additionally, onboard bottle incubation experiments will be carried out to determine which nutrients (nitrogen, phosphorus, silicate, vitamins) may limit primary production and shape the phytoplankton community composition. Results obtained from this project will highlight possible plankton community shifts and their drivers and help predict future consequences of global warming in these two sensitive and changing arctic ecosystems. Data are in CSV format. This dataset is MSR/RATS cruise U2023-011 (Ponant RN035) as part of the World data center for oceanography.
DOI: 10.25921/e6h8-d679
title: Catch statistics - details collected by bottom trawl from the fishing vessel Mersey Venture and CCGS Captain Jacques Cartier in Georges Bank, Bay of Fundy, and Scotian Shelf from 2023-02-08 to 2023-03-29 (NCEI Accession 0294336)

description: This dataset contains set level data, catch data, and detailed observations, including bottom temperature and salinity. This is MSR/RATS cruise U2022-050 as part of the World Data Center for oceanography. Data are in CSV format.
DOI: 10.25921/hq92-cy64
title: Catch statistics - details collected by bottom trawl from the CGGS Teleost and CGGS Jon Cabot in Georges Bank, Bay of Fundy, and Scotian Shelf from 2024-03-01 to 2024-04-02 (NCEI Accession 0294337)

description: This dataset contains set level data, catch data, and detailed observations, including bottom T and S. This is MSR/RATS cruise U2023-024 as part of the World Data Center for oceanography. Data are in CSV format.
DOI: 10.25921/3tp2-3h76
title: Fishery survey - catch measurements - details collected by bottom trawl from the CCGS Captain Jacques Cartier in Georges Bank from 2022-03-28 to 2022-04-12 (NCEI Accession 0294338)

description: Set level data, catch data and detailed measurements from bottom trawl survey, including bottom temperature and salinity. This is MSR/RATS cruise U2021-019 as part of the World Data Center for oceanography. Data are in CSV format.
DOI: 10.25921/xg8q-nb73
title: Physical (Hydrography), chemical (CTD), and biological (Water Quality) processes of the Texas-Louisiana continental shelf, 2020 (NCEI Accession 0294428)

description: Two sets of CTD data were taken during the 2020 Shelfwide Hypoxia cruise off the Louisiana continental shelf. Hydrographic data were obtained with the LUMCON SeaBird 911+ CTD system and a YSI 6820. Nutrient, surface salinity, Secchi depth, Winkler results, and station information data were also acquired. Note that aspects of this year’s cruise were restricted due to the covid-19 pandemic. Only a limited number of vessel and scientific crew were allowed onboard, which meant that 24 hour operations were not possible. Collected parameters were also scaled back (suspended sediments and pigments were not sampled). Also, Mississippi River stations were not visited.
DOI: 10.25921/8g2w-3b56
title: Physical (Hydrography), chemical (CTD), and biological (Water Quality) processes of the Texas-Louisiana continental shelf, 2021 (NCEI Accession 0294429)

description: Two sets of CTD data were taken during the 2021 Shelfwide Hypoxia cruise off the Louisiana continental shelf. Hydrographic data were obtained with the LUMCON SeaBird 911+ CTD system and a YSI EXO3. Nutrient, pigment, suspended sediment, surface salinity, Secchi depth, Winkler results, and station information data were also acquired. PAR data were not collected in the 2021 dataset due to a cable malfunction at the first station on the cruise which also meant that CPAR data could not be included.

Station location information is located in the 2021_StationLog.xlsx with metadata for each station in subsequent spreadsheets.
DOI: 10.25921/24hv-6w93
title: Water temperature, salinity, and others taken by CTD from the research vessel Weatherbird II in Gulf of Mexico from 2023-05-23 to 2023-05-31 (NCEI Accession 0294432)

description: This dataset includes CTD and environmental data for four stations collected onboard R/V Weatherbird II cruise WB-0523 in the Gulf of Mexico from 2023-05-23 to 2023-05-31. The dataset includes profiles/casts of temperature, salinity, conductivity, chlorophyll-a and colored dissolved organic matter fluorescence, turbidity, oxygen saturation, sound velocity, altimetry and Photosynthetically Available Radiation (PAR). R/V Weatherbird II cruise WB-0523 was led by chief scientists Dr. Patrick Schwing, Dr. Rebekka Larson, and Dr. Gregg Brooks. Processed data are in CNV format.
DOI: 10.25921/6hea-tg09
title: Water temperature, salinity, and others taken by CTD from the research vessel Weatherbird II in Gulf of Mexico from 2022-05-16 to 2022-05-19 (NCEI Accession 0294433)

description: This dataset includes CTD and environmental data for four stations collected onboard R/V Weatherbird II cruise WB-0522 in the Gulf of Mexico from 2022-05-16 to 2022-05-19. The dataset includes 4 profiles/casts of temperature, salinity, conductivity, chlorophyll-a and colored dissolved organic matter fluorescence, turbidity, oxygen saturation, sound velocity, altimetry and Photosynthetically Available Radiation (PAR). R/V Weatherbird II cruise WB-0522 was led by chief scientists Dr. Patrick Schwing, Dr. Rebekka Larson, and Dr. Gregg Brooks. Processed data are in text format.