cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15468212
title: OMI Overpass files for NO2, O3, HCHO in 7zip format

description: OMI satellite overpass data set in 7zip format. The data are in Ascii format with meta data at the top of each file. The data are for total column NO2, HCHO, and OZONE.
DOI: 10.5281/zenodo.15468213
title: OMI Overpass files for NO2, O3, HCHO in 7zip format

description: OMI satellite overpass data set in 7zip format. The data are in Ascii format with meta data at the top of each file. The data are for total column NO2, HCHO, and OZONE.
DOI: 10.5281/zenodo.16930160
title: Covers abkhaz 6-15
DOI: 10.5281/zenodo.16930161
title: Covers abkhaz 6-15
DOI: 10.15468/dl.fcwrgb
title: Occurrence Download

description: A dataset containing 642 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-75.92251 4.7997,-74.62746 4.7997,-74.62746 5.77918,-75.92251 5.77918,-75.92251 4.7997))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 642 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033504-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vj243m
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallonia pulchella",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033507-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5qnymq
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-75.92251 4.7997,-74.62746 4.7997,-74.62746 5.77918,-75.92251 5.77918,-75.92251 4.7997))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Testudines"
 ]
}

 The dataset includes 50 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033508-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cheecg
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallonia pulchella",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033505-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fv6nyv
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallonia pulchella",
 "Country is Israel",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033506-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tksket
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Anablepsoides lungi)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 24 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033509-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.upp6u4
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-75.92251 4.7997,-74.62746 4.7997,-74.62746 5.77918,-75.92251 5.77918,-75.92251 4.7997))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Crocodylia"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033510-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7kapbh
title: Occurrence Download

description: A dataset containing 19187 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Acacia myrtifolia"
 ]
}

 The dataset includes 19187 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033511-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekq8xf
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallonia pulchella",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033512-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.au6z7r
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallonia pulchella",
 "Country is Uruguay",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033514-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16930142
title: Brazilian urban forests database for cities with more than 100,000 inhabitants

description: Occurrence of urban forests in Brazilian cities with more than 100,000 inhabitants separated into biomes for use in climate modelling.
DOI: 10.5281/zenodo.16930143
title: Brazilian urban forests database for cities with more than 100,000 inhabitants

description: Occurrence of urban forests in Brazilian cities with more than 100,000 inhabitants separated into biomes for use in climate modelling.
DOI: 10.15468/dl.f6jku8
title: Occurrence Download

description: A dataset containing 15907 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Acacia terminalis"
 ]
}

 The dataset includes 15907 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033513-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fae72c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gulaphallus falcifer)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033515-250811113504898/datasets/export for details.
DOI: 10.15468/dl.7qhr3z
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dictyonella hirta",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 26 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033516-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29321198
title: Lizard and sea turtle skin fibroblast primary cells: metabolomic and mitochondrial network data

description: Research studying how primary cells derived from sea turtles (<i>Caretta caretta</i>, CC) and lizards (<i>Sceloporus occidentalis, </i>LP) cope with extended hypoxia exposure. Metabolomic data and mitochondrial network data.
DOI: 10.6084/m9.figshare.29321198.v1
title: Lizard and sea turtle skin fibroblast primary cells: metabolomic and mitochondrial network data

description: Research studying how primary cells derived from sea turtles (<i>Caretta caretta</i>, CC) and lizards (<i>Sceloporus occidentalis, </i>LP) cope with extended hypoxia exposure. Metabolomic data and mitochondrial network data.
DOI: 10.15468/dl.334skq
title: Occurrence Download

description: A dataset containing 10043 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Anolis cristatellus"
 ]
}

 The dataset includes 10043 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033520-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2zg9hp
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Guianacara geayi)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 57 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033519-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ukswy
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cliona celata",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033521-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evkw5a
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Halichondria panicea",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 32 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033525-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jctksj
title: Occurrence Download

description: A dataset containing 109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Clarias pachynema)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 109 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033523-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y2q4p6
title: Occurrence Download

description: A dataset containing 341 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence, Observation, Machine Observation)",
 "Geometry POLYGON((-60 -35,-33 -35,-33 -1,-60 -1,-60 -35))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Microgramma squamulosa, Microgramma squamulosa)",
 "Year 2020-2025"
 ]
}

 The dataset includes 341 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033522-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f5t8nd
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Halichondria panicea",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033524-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.exfd6h
title: Occurrence Download

description: A dataset containing 432 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Oxaea flavescens"
 ]
}

 The dataset includes 432 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033527-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b5ffaw
title: Occurrence Download

description: A dataset listing the 109625 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "TaxonKey is Insecta"
 ]
}

 The dataset's 109625 records were derived from 613 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033517-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10390549
title: Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction

description: This Zenodo repository provides comprehensive resources for the paper titled "Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction" published on Bioinformatics. We created a dataset of 63,000 molecular dynamics simulations by performing 10 simulations of 10 ns on 6,300 complexes. Neural networks were developed to learn from this data in order to predict the binding affinities of protein-ligand complexes. The implementation of these neural networks are available on github. Our collection includes training/benchmark datasets, trained statistical models, and results on test sets (CSV & PDF files).

 

Training/benchmark datasets:

Training, validation and test sets are provided to train and evaluate the following neural networks:



Pafnucy, Proli and Densenucy without MD data augmentation (dataset file names contain "initial")

Pafnucy, Proli and Densenucy with MD data augmentation (dataset file names contain "MDDA")

Pafnucy with/without MD data augmentation and Proli and Densenucy with MD data augmentation were also evaluated on the fep test set (test set file name contain "fep")

Timenucy and Videonucy using spatiotemporal learning methods (dataset file names contain "4D")

Pafnucy without MD data augmentation and on a reduced training set (dataset file names contain "reduced")


For each training methodology (MD data augmentation and spatiotemporal learning), we provide the data for the whole complex, only the ligand or only the protein. Additionally for spatiotemporal learning, we provide the data with only the ligand using the tracking mode.

 

Statistical models:

We provide the models trained with Pafnucy, Proli, Densenucy, Timenucy and Videonucy. Each models were trained in 10 replicates. 

For Pafnucy, Proli, Densenucy, we provide the models trained with random and systematic rotations, as well as with or without MD data augmentation.

For Proli, Densenucy, Timenucy and Videonucy, we provide the models trained on the whole complex, only the ligand or only the protein.

For Pafnucy we also provide the models trained on the reduced set (5932 complexes).

 

Results on test sets (CSV & PDF files):

We provide the predictions on the PDBbind v.2016 core set.



For spatiotemporal learning methods (Timenucy and Videonucy), there are predictions for only 83 complexes, as we did not perform simulations on the whole test set.

For models trained with MD DA, predictions were carried on the crystallographic structures as well as on the frames extracted from the simulations performed on the test set (augmented test).


Results on the FEP dataset are also provided for Pafnucy, Proli and Densenucy.

 

The Raw MD data (~4.5 To) are stored, and can be visualized/downloaded, on the MDDB.

This work was performed using HPC resources from GENCI-IDRIS (Grant 2021-A0100712496 & 2022-AD011013521) and CRIANN (Grant 2021002).
DOI: 10.5281/zenodo.10390550
title: Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction

description: This Zenodo repository provides comprehensive resources for the paper titled "Spatio-temporal learning from molecular dynamics simulations for protein-ligand binding affinity prediction" published on Bioinformatics. We created a dataset of 63,000 molecular dynamics simulations by performing 10 simulations of 10 ns on 6,300 complexes. Neural networks were developed to learn from this data in order to predict the binding affinities of protein-ligand complexes. The implementation of these neural networks are available on github. Our collection includes training/benchmark datasets, trained statistical models, and results on test sets (CSV & PDF files).

 

Training/benchmark datasets:

Training, validation and test sets are provided to train and evaluate the following neural networks:



Pafnucy, Proli and Densenucy without MD data augmentation (dataset file names contain "initial")

Pafnucy, Proli and Densenucy with MD data augmentation (dataset file names contain "MDDA")

Pafnucy with/without MD data augmentation and Proli and Densenucy with MD data augmentation were also evaluated on the fep test set (test set file name contain "fep")

Timenucy and Videonucy using spatiotemporal learning methods (dataset file names contain "4D")

Pafnucy without MD data augmentation and on a reduced training set (dataset file names contain "reduced")


For each training methodology (MD data augmentation and spatiotemporal learning), we provide the data for the whole complex, only the ligand or only the protein. Additionally for spatiotemporal learning, we provide the data with only the ligand using the tracking mode.

 

Statistical models:

We provide the models trained with Pafnucy, Proli, Densenucy, Timenucy and Videonucy. Each models were trained in 10 replicates. 

For Pafnucy, Proli, Densenucy, we provide the models trained with random and systematic rotations, as well as with or without MD data augmentation.

For Proli, Densenucy, Timenucy and Videonucy, we provide the models trained on the whole complex, only the ligand or only the protein.

For Pafnucy we also provide the models trained on the reduced set (5932 complexes).

 

Results on test sets (CSV & PDF files):

We provide the predictions on the PDBbind v.2016 core set.



For spatiotemporal learning methods (Timenucy and Videonucy), there are predictions for only 83 complexes, as we did not perform simulations on the whole test set.

For models trained with MD DA, predictions were carried on the crystallographic structures as well as on the frames extracted from the simulations performed on the test set (augmented test).


Results on the FEP dataset are also provided for Pafnucy, Proli and Densenucy.

 

The Raw MD data (~4.5 To) are stored, and can be visualized/downloaded, on the MDDB.

This work was performed using HPC resources from GENCI-IDRIS (Grant 2021-A0100712496 & 2022-AD011013521) and CRIANN (Grant 2021002).
DOI: 10.15468/dl.x77yjq
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Copadichromis azureus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033528-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8bwbdq
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hymeniacidon perlevis",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033529-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vak5ww
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hymeniacidon perlevis",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 36 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033530-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qzj9tq
title: Occurrence Download

description: A dataset containing 80194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is COL.33.1_2",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 80194 records from 213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033501-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9azs4y
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Diplocheilichthys pleurotaenia)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033531-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.