cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13750967
title: GraphaRNA dataset and model

description: Graph Neural Network and Diffusion Model for Modeling RNA Interatomic Interactions

This repository contains the datasets and the pre-trained model associated with GraphaRNA, a diffusion-based graph neural network for RNA 3D structure prediction. The data is organized into multiple files, each providing key resources for training, validation, and testing the model, as well as a pre-trained model ready for inference.

Data Overview:





rRNA_tRNA.tar.gz:



Contains raw PDB files with extracted descriptors from ribosomal RNA (rRNA) and transfer RNA (tRNA) structures.





non_rRNA_tRNA.tar.gz:



Contains raw PDB files with extracted descriptors from RNA molecules that are non-rRNA and non-tRNA. These serve as a separate test set.





train-pkl.tar.gz:



Contains the filtered and preprocessed pickle files for the training set, derived from the rRNA_tRNA dataset. These files are used to train GraphaRNA.





val-pkl.tar.gz:



Contains the validation set, which is a subset of the training data from train-pkl.tar.gz.





test-pkl.tar.gz:



Contains the preprocessed pickle files for the test set, derived from the non_rRNA_tRNA dataset. This set includes RNA descriptors that are not rRNA or tRNA, providing a challenging test scenario.





model_epoch_800.tar.gz:



Contains the pre-trained GraphaRNA model after 800 epochs of training on the train-pkl dataset. This model is ready for inference and evaluation.




Use of Data and Model:



The raw PDB files can be used for RNA descriptor extraction, while the pickle files are preprocessed for direct use in training, validation, and testing workflows.

The GraphaRNA model in model_epoch_800.tar.gz can be used to run inference on new RNA data or to reproduce results from the associated paper.


How to Use:



Training: The train-pkl.tar.gz contains data that can be used to retrain the GraphaRNA model from scratch.

Validation: The val-pkl.tar.gz can be used to validate the model during or after training.

Testing: Use the test-pkl.tar.gz to evaluate the model's performance on RNA types that it wasn't trained on (non-rRNA and non-tRNA).

Inference: The model_epoch_800.tar.gz is ready for inference on new RNA sequences.


Acknowledgments:

If you use this dataset or the pre-trained model in your research, please cite the associated paper (linked here once published).
DOI: 10.15468/dl.fyjbhx
title: Occurrence Download

description: A dataset containing 1558 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"TAXON_KEY","value":"2476643","matchCase":false},{"type":"equals","key":"HAS_COORDINATE","value":"true","matchCase":false},{"type":"equals","key":"BASIS_OF_RECORD","value":"PRESERVED SPECIMEN","matchCase":false},{"type":"equals","key":"CONTINENT","value":"southamerica","matchCase":false}]}

 The dataset includes 1558 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008030-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hkaztf
title: Occurrence Download

description: A dataset containing 7084904 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "PublishingOrg is ff90b050-c256-11db-b71b-b8a03c50a862"
 ]
}

 The dataset includes 7084904 records from 1011 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008116-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-2097796364
title: Joint-Structural Biology Group (JSBG) BAG proposal for ID29 beamline

description: The aim of the JSBG BAG proposal for ID29 beamline is to develop new methods for time-resolved serial crystallography experiments at 4th generation source and to study time dependent structural conformation of biological macromolecules that are studies at the ESRF-EMBL-GR Joint Structural Biology Group. Method developments include the study of radiation damage at high flux densities and with partially polychromatic beam (1% and 0.3%), the implementation and development of various sample delivery methods - mixing in capillary, microfluidics, tape-drive and fixed targets. This further includes development of GPU-based indexing algorithm, data reduction software, and develop new data collection strategies for pump-probe SSX experiments integrating nanosecond laser. Biological systems include the study of photoactivatable proteins, enzymatic systems through mixing experiments and multi-temperature jump experiments to study protein dynamics.
DOI: 10.17882/101468
title: DMS/O/P cycling in coastal NE subarctic Pacific phytoplankton assemblages exposed to elevated irradiance and photosynthetic inhibition (2022-2023)

description: This dataset is associated with the article "A potential photo-protective, antioxidant function for DMSO in marine phytoplankton" accepted for publication in PLOS ONE. The primary data consists of concentrations and biological turnover rates from native and isotopically-labelled (D3/D6/13C) DMSP, DMS and DMSO tracers in 10 deck-board incubation experiments using natural phytoplankton assemblages in the NE subarctic Pacific (i.e. coastal Vancouver Island, BC, Canada). The data includes results from experiments manipulating surface irradiance exposure (low vs. high light) in phytoplankton assemblages taken from variable depths to simulate the effects of vertical mixing-induced photic stress (n = 7), as well as photosynthethic electron transport inhibition experiments (n = 3) using the inhibitior DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea). Ancillary data includes photo-physiology measurements (i.e. the maximum quantum yield of photochemistry at PSII, Fv/Fm, and Stern-Volmer non-photochemical quenching, NPQsv), HPLC pigments, and CHEMTAX input parameters and outputs used to derive phytoplankton community composition in some experiments.
DOI: 10.15468/dl.s7qjjr
title: Occurrence Download

description: A dataset containing 3501 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Parnassius apollo (Linnaeus, 1758)",
 "Year 2010-2025"
 ]
}

 The dataset includes 3501 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008033-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uajsrx
title: Occurrence Download

description: A dataset containing 820 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Copernicia alba Morong"
 ]
}

 The dataset includes 820 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008034-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.46g79y
title: Occurrence Download

description: A dataset containing 986 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "DatasetKey is Données invertébrés saisies sous BioloVision Auvergne-Rhône-Alpes - VisioNature opportuniste",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Parnassius apollo (Linnaeus, 1758)",
 "Year 2010-2025"
 ]
}

 The dataset includes 986 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008122-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ww9sup
title: Occurrence Download

description: A dataset containing 1558 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"TAXON_KEY","value":"2476643","matchCase":false},{"type":"equals","key":"HAS_COORDINATE","value":"true","matchCase":false},{"type":"equals","key":"BASIS_OF_RECORD","value":"PRESERVED SPECIMEN","matchCase":false},{"type":"equals","key":"CONTINENT","value":"southamerica","matchCase":false}]}

 The dataset includes 1558 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008035-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26093/cds/aladin/175v-35h
title: VISIONS DR2 Ks band HiPS

description: VISIONS - VISTA Star Formation Atlas is a near-infrared (NIR) VISTA public survey covering all major nearby star-forming regions accessible from the southern hemisphere. The survey is designed to deliver deep high-sensitivity observations of areas with large amounts of extinction, control fields which sample the predominant stellar populations in largely extinction-free regions, and wide field data in multiple epochs on large areas surrounding the targeted star-forming regions. This data release contains all collected observations from April 2017 to October 2021 on the Corona Australis star-forming region for a total of 3360 submitted files. The area covered amounts to about 43 deg2.
DOI: 10.5281/zenodo.14989911
title: 2024 Drivable street network around Joao Pessoa with Ponte do Futuro intervention project

description: This file was captured from OSM (Open Street Map) and then prepared and adjusted to add an intervention, in the following way, The OSM drivable network with a 46 km network distance catchment from João Pessoa was downloaded via OSMnx (in 2024), then this edge file was converted into planar CRS (EPSG:31985 - SIRGAS 2000/ UTM zone 25S), then simplified with Douglas-Peucker method qith a 5 meters tolerance, then the Future Bridge Intervention (Complexo Ponte do Futuro) routes were drawn using as base information and images in this Newspaper Article: https://g1.globo.com/pb/paraiba/noticia/2024/07/06/ponte-cabedelo-lucena-fase-de-escolha-de-propostas-para-obra-e-concluida-pelo-governo-da-pb.ghtml

Satellite images available in 2024 via QGIS QuickMapServices were used for land images, to help locate routes vehiculated in the Newspaper Article.

The 46km network distance cacthment  from João Pessoa was chosen as it comprehends up to Lucena municipality, the furhest municipality from João Pessoa that will receive the Ponte do Futuro intervention, the cacthment approximates partially João Pessoa Metropolitan Region.
DOI: 10.5281/zenodo.14989912
title: 2024 Drivable street network around Joao Pessoa with Ponte do Futuro intervention project

description: This file was captured from OSM (Open Street Map) and then prepared and adjusted to add an intervention, in the following way, The OSM drivable network with a 46 km network distance catchment from João Pessoa was downloaded via OSMnx (in 2024), then this edge file was converted into planar CRS (EPSG:31985 - SIRGAS 2000/ UTM zone 25S), then simplified with Douglas-Peucker method qith a 5 meters tolerance, then the Future Bridge Intervention (Complexo Ponte do Futuro) routes were drawn using as base information and images in this Newspaper Article: https://g1.globo.com/pb/paraiba/noticia/2024/07/06/ponte-cabedelo-lucena-fase-de-escolha-de-propostas-para-obra-e-concluida-pelo-governo-da-pb.ghtml

Satellite images available in 2024 via QGIS QuickMapServices were used for land images, to help locate routes vehiculated in the Newspaper Article.

The 46km network distance cacthment  from João Pessoa was chosen as it comprehends up to Lucena municipality, the furhest municipality from João Pessoa that will receive the Ponte do Futuro intervention, the cacthment approximates partially João Pessoa Metropolitan Region.
DOI: 10.15468/dl.98czt4
title: Occurrence Download

description: A dataset containing 60072 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lama guanicoe (Müller, 1776)"
 ]
}

 The dataset includes 60072 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008022-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cujphh
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Tolwaka ornata, nuevo género y especie de Salpingidae (Coleoptera) de Chile"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008036-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zn8w7e
title: Occurrence Download

description: A dataset containing 245013 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "OccurrenceStatus is Present",
 "TaxonKey is Capreolus capreolus (Linnaeus, 1758)",
 "Year 2015-2025"
 ]
}

 The dataset includes 245013 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008028-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26093/cds/aladin/37ps-h0d
title: VISIONS DR2 H band HiPS

description: VISIONS - VISTA Star Formation Atlas is a near-infrared (NIR) VISTA public survey covering all major nearby star-forming regions accessible from the southern hemisphere. The survey is designed to deliver deep high-sensitivity observations of areas with large amounts of extinction, control fields which sample the predominant stellar populations in largely extinction-free regions, and wide field data in multiple epochs on large areas surrounding the targeted star-forming regions. This data release contains all collected observations from April 2017 to October 2021 on the Corona Australis star-forming region for a total of 3360 submitted files. The area covered amounts to about 43 deg2.
DOI: 10.5281/zenodo.14986232
title: Dataset with EEG data from Malayalam speakers. (Shalu et al., 2025)

description: Dataset with EEG data from Malayalam speakers. The repository contains raw data as well as data preprocessed in EEGLAB using the preprocessing pipeline script included, which was adapted from Muralikrishnan, R. (2025). The data was collected from 35 first-language speakers of Malayalam, when they read sentences of various types, including intransitive, experiencer and modal constructions, and judged whether the sentences were acceptable, because by design, some sentences were grammatical, whilst others were not. The data is anonymised and does not allow personally identifying specific individuals.

Reference

Muralikrishnan, R. (2025). Preprocessing pipeline for EEG Data using EEGLAB. (Version 1.0). Zenodo. https://doi.org/10.5281/ZENODO.14988778
DOI: 10.5281/zenodo.14986233
title: Dataset with EEG data from Malayalam speakers. (Shalu et al., 2025)

description: Dataset with EEG data from Malayalam speakers. The repository contains raw data as well as data preprocessed in EEGLAB using the preprocessing pipeline script included, which was adapted from Muralikrishnan, R. (2025). The data was collected from 35 first-language speakers of Malayalam, when they read sentences of various types, including intransitive, experiencer and modal constructions, and judged whether the sentences were acceptable, because by design, some sentences were grammatical, whilst others were not. The data is anonymised and does not allow personally identifying specific individuals.

Reference

Muralikrishnan, R. (2025). Preprocessing pipeline for EEG Data using EEGLAB. (Version 1.0). Zenodo. https://doi.org/10.5281/ZENODO.14988778
DOI: 10.15468/dl.psxk64
title: Occurrence Download

description: A dataset containing 1493 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-122.69488 58.13364,-122.72005 58.14442,-122.73946 58.14094,-122.75906 58.12784,-122.76771 58.10018,-122.7649 58.08034,-122.75806 58.0601,-122.74466 58.04933,-122.72889 58.04433,-122.71366 58.04014,-122.70327 58.04074,-122.69269 58.04101,-122.6843 58.04336,-122.66551 58.06112,-122.66087 58.08391,-122.66304 58.10138,-122.66633 58.11237,-122.67503 58.12177,-122.68516 58.12811,-122.69028 58.13078,-122.69488 58.13364))",
 "Geometry POLYGON((-122.58963 58.20541,-122.57561 58.22,-122.56909 58.23847,-122.56889 58.25534,-122.57465 58.27263,-122.59846 58.29413,-122.62036 58.30489,-122.64839 58.30182,-122.66837 58.29221,-122.68412 58.27224,-122.6853 58.23351,-122.66837 58.20733,-122.64468 58.19866,-122.62074 58.19734,-122.60307 58.19926,-122.58963 58.20541))",
 "Geometry POLYGON((-122.70929 58.49494,-122.67115 58.48832,-122.65326 58.49861,-122.63589 58.52381,-122.63222 58.54559,-122.64103 58.56565,-122.66305 58.58546,-122.67724 58.59231,-122.70317 58.59134,-122.72641 58.57715,-122.73326 58.55635,-122.73473 58.538,-122.73082 58.51354,-122.72152 58.50301,-122.70929 58.49494))",
 "Geometry POLYGON((-122.66958 58.77262,-122.68637 58.77319,-122.70601 58.76465,-122.71454 58.74587,-122.71682 58.72282,-122.71426 58.70604,-122.6784 58.70034,-122.64995 58.70575,-122.64113 58.72681,-122.64113 58.75242,-122.66019 58.76921,-122.66958 58.77262))",
 "Geometry POLYGON((-123.14898 58.84904,-123.11312 58.86105,-123.09746 58.89874,-123.10772 58.92245,-123.14926 58.94522,-123.17714 58.9504,-123.20646 58.94408,-123.22894 58.93639,-123.23889 58.91654,-123.24515 58.89064,-123.22523 58.85991,-123.18767 58.84796,-123.14898 58.84904))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1493 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008123-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wc4enb
title: Occurrence Download

description: A dataset containing 149209 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Invertebrate Zoology Division, Yale Peabody Museum"
 ]
}

 The dataset includes 149209 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008032-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26093/cds/aladin/gp59-91
title: VISIONS DR2 J band HiPS

description: VISIONS - VISTA Star Formation Atlas is a near-infrared (NIR) VISTA public survey covering all major nearby star-forming regions accessible from the southern hemisphere. The survey is designed to deliver deep high-sensitivity observations of areas with large amounts of extinction, control fields which sample the predominant stellar populations in largely extinction-free regions, and wide field data in multiple epochs on large areas surrounding the targeted star-forming regions. This data release contains all collected observations from April 2017 to October 2021 on the Corona Australis star-forming region for a total of 3360 submitted files. The area covered amounts to about 43 deg2.
DOI: 10.26093/cds/aladin/17yr-vnb
title: VISIONS DR2 color (from bands Ks, H, J) HiPS

description: VISIONS - VISTA Star Formation Atlas is a near-infrared (NIR) VISTA public survey covering all major nearby star-forming regions accessible from the southern hemisphere. The survey is designed to deliver deep high-sensitivity observations of areas with large amounts of extinction, control fields which sample the predominant stellar populations in largely extinction-free regions, and wide field data in multiple epochs on large areas surrounding the targeted star-forming regions. This data release contains all collected observations from April 2017 to October 2021 on the Corona Australis star-forming region for a total of 3360 submitted files. The area covered amounts to about 43 deg2.
DOI: 10.15468/dl.bp7pdx
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyttarops alecto Thomas, 1913"
 ]
}

 The dataset includes 61 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008124-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6p6kt
title: Occurrence Download

description: A dataset containing 1202 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Penaeus merguiensis De Man, 1888"
 ]
}

 The dataset includes 1202 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008041-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fpfk7d
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Tolwaka ornata, nuevo género y especie de Salpingidae (Coleoptera) de Chile"
 ]
}

 The dataset's 1 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008039-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwtvdq
title: Occurrence Download

description: A dataset containing 1039 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Argentina, Paraguay)",
 "TaxonKey is Forpus passerinus (Linnaeus, 1758)",
 "Year 1000-2024"
 ]
}

 The dataset includes 1039 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008130-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wtn9yh
title: Occurrence Download

description: A dataset containing 1661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Paraguay, Argentina)",
 "TaxonKey is Pyrrhura leucotis (Kuhl, 1820)",
 "Year 1000-2024"
 ]
}

 The dataset includes 1661 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008127-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xq998y
title: Occurrence Download

description: A dataset containing 461788 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Frangula alnus Mill.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 461788 records from 1706 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008031-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.