cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16742296
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.



 all-outputs.txt:



Contains basic metadata about all descriptors: name of file, number of segments, number of nucleotides, sequence of each segment, and positions of segments in original PDB files.



grapharna.tar:



Docker image of GraphaRNA instance.




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.r94t6t
title: Occurrence Download

description: A dataset containing 838 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Microptilotis albonotatus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 838 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013693-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.72g7u7
title: Occurrence Download

description: A dataset containing 4809 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Microptilotis analogus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 4809 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013694-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phpt9a
title: Occurrence Download

description: A dataset containing 1414 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Doryrhamphus excisus"
 ]
}

 The dataset includes 1414 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013695-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eak9q2
title: Occurrence Download

description: A dataset containing 483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Microptilotis cinereifrons)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 483 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013697-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9w8qr4
title: Occurrence Download

description: A dataset containing 1349962 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fabaceae",
 "Geometry POLYGON ((26.04335 1.226334, 135.0263 1.226334, 135.0263 55.38525, 26.04335 55.38525, 26.04335 1.226334))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1349962 records from 785 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013666-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7nffj2
title: Occurrence Download

description: A dataset containing 179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aedes aegypti",
 "Country is Cuba",
 "HasCoordinate is true"
 ]
}

 The dataset includes 179 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013698-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rsvgjn
title: Occurrence Download

description: A dataset containing 14698 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Aristida adscensionis"
 ]
}

 The dataset includes 14698 records from 359 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013696-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4xu5kn
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aedes aegypti",
 "Country is Dominica",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013699-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmjtsx
title: Occurrence Download

description: A dataset containing 3927 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is South Africa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Danaus chrysippus"
 ]
}

 The dataset includes 3927 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013700-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gt4j6w
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Vipera aspis)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013702-250802193616735/datasets/export for details.
DOI: 10.15468/dl.q8339t
title: Occurrence Download

description: A dataset containing 35103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Vipera aspis)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 35103 records from 797 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013701-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jqvc3r
title: Occurrence Download

description: A dataset containing 504 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Tapirus pinchaque (Roulin, 1829)"
 ]
}

 The dataset includes 504 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008201-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ycst42
title: Occurrence Download

description: A dataset containing 1176 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aristeus antennatus (Risso, 1816)"
 ]
}

 The dataset includes 1176 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008203-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h24nzd
title: Occurrence Download

description: A dataset containing 1199469 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sylvia curruca (Linnaeus, 1758)"
 ]
}

 The dataset includes 1199469 records from 1281 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008167-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n4hmcs
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dinomys branickii Peters, 1873"
 ]
}

 The dataset's 1 records were derived from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004357-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4cb3g3
title: Occurrence Download

description: A dataset containing 1387 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "TaxonKey is Cervus elaphus"
 ]
}

 The dataset includes 1387 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027376-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xf6wgp
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Locality is one of (Tonneins, Tonneins (Lot-et-Garonne), Tonneins (Lot-et-geronne), Tonneins (ville))",
 "Year 2016-2026"
 ]
}

 The dataset includes 47 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027379-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ypx5p
title: Occurrence Download

description: A dataset containing 4627 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Artemisia annua",
 "Continent is Europe",
 "HasCoordinate is true",
 "CoordinateUncertaintyInMeters is less than or equal to 100",
 "Year is greater than or equal to 1970",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "not" : {
 "BasisOfRecord" : [
 "is Material citation"
 ]
 }
 }
 ]
}

 The dataset includes 4627 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027380-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5a53zx
title: Occurrence Download

description: A dataset containing 266 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhyncomya columbina"
 ]
}

 The dataset includes 266 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027381-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25625/mqtmbi
title: Smartup Data Management Plan Ethics

description: Smartup Data Management Plan
DOI: 10.5281/zenodo.18682369
title: Thermographic data for manuscript Mus.3154-D-5 (SLUB)

description: This data set contains thermographic images for the visualisation of watermarks. An IRCAM Equus 327k with Watermark Imager software (Fraunhofer) version 8.416 (R2016b) was used.
DOI: 10.5281/zenodo.18682368
title: Thermographic data for manuscript Mus.3154-D-5 (SLUB)

description: This data set contains thermographic images for the visualisation of watermarks. An IRCAM Equus 327k with Watermark Imager software (Fraunhofer) version 8.416 (R2016b) was used.
DOI: 10.15468/dl.jexssn
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Clinopodium nepalense"
 ]
}

 The dataset includes 75 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027382-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zkg7ju
title: Occurrence Download

description: A dataset containing 20 records in GBIF matching the query:
SELECT DISTINCT
 latestperiodorhighestsystem.concept latestperiodorhighestsystem,
 CONCAT_WS(' -&gt; ', latestperiodorhighestsystem.lineage) lineage
FROM
 occurrence

 The dataset's 20 records were derived from 89014 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027356-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23708/wy1fyl
title: DNA metabarcoding analysis of the African wolf (Canis lupaster) diet

description: In this study, we characterised for the first time through DNA metabarcoding the omnivorous diet of the African wolf. Metabarcoding raw data (c. 3.4 Gb; paird-read) were generated from 29 faecal samples of African wolf (Canis lupaster) collected in spring / summer 2016 in the province of Tlemcen, northwestern Algeria. Three genes were amplified and co-sequenced to study the omnivorous diet of the species: 12S for vertebrates (Riaz et al. 2011; https://doi.org/10.1093/nar/gkr732), COI for arthropods (Zeale et al. 2011; https://doi.org/10.1111/j.1755-0998.2010.02920.x), trnl for plants (Taberlet et al. 2007; https://doi.org/10.1093/nar/gkl938). DNA extraction was carried out from a subsample of c. 200 mg of each faeces using the QIAamp DNA Stool kit (Qiagen, Les Ulis, France) within the “Degraded DNA” platform of the Institut des Sciences de l'Evolution de Montpellier (ISEM). In order to capture the broad dietary spectrum of the African wolf, three genetic markers were used to detect vertebrates (mitochondrial 12S ribosomal RNA—12S), arthropods (mitochondrial Cytochrome Oxidase subunit I—COI) and plants (chloroplastic trnl intron—trnl). The amplicon libraries were built following a two-step amplification procedure adapted from the Illumina 16S Metagenomic Sequencing Library Preparation Guide (ref.15044223 rev. B). After purification with magnetic beads (ratio: 1.5 X), PCR products were quantified with QuantiFluor® dsDNA System, and the final equimolar pool was sequenced on a MiSeq Illumina sequencer using the Reagent kit v2 (300 cycles).
DOI: 10.15468/dl.4skkqv
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Clinopodium euosmum"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027383-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ph89wv
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abies cilicica isaurica"
 ]
}

 The dataset includes 32 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027384-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cefcb9
title: Occurrence Download

description: A dataset containing 11760182 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Occurrence evidence)",
 "Geometry POLYGON((-76.63732 15.75103,-83.75563 1.20811,-81.55235 -14.56383,-70.87489 -21.01493,-58.84156 -23.36863,-49.01152 -18.78402,-36.13077 -13.57745,-33.758 2.73251,-46.97772 17.21364,-76.63732 15.75103))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 11760182 records from 1621 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027330-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d7ywq5
title: Occurrence Download

description: A dataset containing 1130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Platynota rostrana (Walker, 1863))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1130 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072938-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gvs5aa
title: Occurrence Download

description: A dataset containing 5865 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Galemys pyrenaicus (É.Geoffroy Saint-Hilaire, 1811)"
 ]
}

 The dataset includes 5865 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072937-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vrz9gd
title: Occurrence Download

description: A dataset containing 1326 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ptycholomoides aeriferana (Herrich-Schäffer, 1851))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1326 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072940-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y4g8ty
title: Occurrence Download

description: A dataset containing 20466341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ClassKey is Mammalia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Material sample, Material citation, Fossil, Living Specimen, Specimen)"
 ]
 }
 },
 {
 "not" : {
 "CoordinateUncertaintyInMeters" : [
 "is one of (301, 3036, 999, 9999)"
 ]
 }
 },
 {
 "not" : {
 "DecimalLatitude" : [
 "is 0"
 ]
 }
 },
 {
 "not" : {
 "DecimalLongitude" : [
 "is 0"
 ]
 }
 },
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 20466341 records from 9180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072924-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wm8p42
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Machlolophus nuchalis)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080148-250717081556266/datasets/export for details.
DOI: 10.15468/dl.f8sz6q
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008005-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.