cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.lylhtk
title: Occurrence Download

description: A dataset containing 611 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hemicircus concretus (Temminck, 1821)"
 ]
}

 The dataset includes 611 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001556-171113114016250/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ty5p7t
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Colección de anfibios y reptiles, Universidad del Valle (Colección UV-C)",
 "TaxonKey is Anolis antonii Boulenger, 1908"
 ]
}

 The dataset includes 26 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0340589-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r3m4hg
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Allium proponticum Stearn & Özhatay"
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026436-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sog4ik
title: Occurrence Download

description: A dataset listing the 1799 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-88.10623 13.1624,-87.88651 13.14903,-87.93869 13.19716,-87.84531 13.22925,-87.7684 13.28807,-87.82059 13.3335,-87.84893 13.33964,-87.84756 13.37271,-87.84531 13.42702,-87.75192 13.36023,-87.68875 13.37092,-87.64755 13.45107,-87.71622 13.47778,-87.7684 13.51784,-87.75192 13.64065,-87.7272 13.74472,-87.7272 13.80874,-87.78488 13.88075,-87.8096 13.92607,-87.92496 13.88874,-88.00735 13.87275,-88.10623 13.62463,-88.10623 13.1624))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 1799 records were derived from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017166-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zbakuw
title: Occurrence Download

description: A dataset containing 388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Charadrius alexandrinus nivosus (Cassin, 1858)"
 ]
}

 The dataset includes 388 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001556-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s45x9n
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Piper obaldianum C.DC."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0189684-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yghzkx
title: Occurrence Download

description: A dataset containing 382 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Chinese Taipei, China)",
 "TaxonKey is Eichhornia crassipes (Mart.) Solms"
 ]
}

 The dataset includes 382 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046914-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tcg3ea
title: Occurrence Download

description: A dataset containing 22418 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbário João de Carvalho e Vasconcellos, I.S.A./U.L."
 ]
}

 The dataset includes 22418 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001556-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmlpnh
title: Occurrence Download

description: A dataset containing 488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Year 2019-2019",
 "Geometry POLYGON((-83.53761 34.53568,-74.54958 34.53568,-74.54958 40.25032,-83.53761 40.25032,-83.53761 34.53568))",
 "HasCoordinate is true",
 "TaxonKey is Cathartes aura (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 488 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017169-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jg5eay
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Mytilopsis leucophaeata (Conrad, 1831)"
 ]
}

 The dataset includes 97 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051331-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pl4vzd
title: Occurrence Download

description: A dataset containing 536 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xyleborus affinis Eichhoff, 1868"
 ]
}

 The dataset includes 536 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001557-150221044754056/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lwuw5p
title: Occurrence Download

description: A dataset containing 431690 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Himantopus himantopus (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 431690 records from 264 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021488-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kvhpwu
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (CHN.15_1, CHN.31_1, CHN.1_1, CHN.24_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Heptacodium miconioides Rehder"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054505-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dpofe9
title: Occurrence Download

description: A dataset containing 1000112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spizella passerina (Bechstein, 1798)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1000112 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001557-150330110031120/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wx536b
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Clarifications of the identities of Paguristes balanophilus Alcock, 1905 and P. calvus Alcock, 1905 (Crustacea, Decapoda, Anomura, Paguroidea, Diogenidae), and the description of another broadly distributed new species"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0340497-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.stdmc3
title: Occurrence Download

description: A dataset containing 12520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "Country is Virgin Islands (U.S.)"
 ]
}

 The dataset includes 12520 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001557-150504100648427/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d5nnqs
title: Occurrence Download

description: A dataset containing 6810000 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2010-2023"
 ]
}

 The dataset includes 6810000 records from 386 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053538-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11237634
title: Conformer datasets for "Equivariant Graph Neural Networks for Toxicity Prediction"

description: Predictive modeling of toxicity is a crucial step in the drug discovery pipeline. It can help filter out molecules with a high probability of failing in the early stages of de novo drug design. Thus, several machine learning (ML) models have been developed to predict the toxicity of molecules by combining classical ML techniques or deep neural networks with well-known molecular representations such as fingerprints or 2D graphs. But the more natural, accurate representation of molecules is expected to be defined in physical 3D space like in ab initio methods. Recent studies successfully used equivariant graph neural networks (EGNNs) for representation learning based on 3D structures to predict quantum-mechanical properties of molecules. Inspired by this, we investigated the performance of EGNNs to construct reliable ML models for toxicity prediction. We used the equivariant transformer (ET) model in TorchMD-NET for this. Eleven toxicity data sets taken from MoleculeNet, TDCommons, and ToxBenchmark have been considered to evaluate the capability of ET for toxicity prediction. Our results show that ET adequately learns 3D representations of molecules that can successfully correlate with toxicity activity, achieving good accuracies on most data sets comparable to state-of-the-art models. We also test a physicochemical property, namely, the total energy of a molecule, to inform the toxicity prediction with a physical prior. However, our work suggests that these two properties can not be related. We also provide an attention weight analysis for helping to understand the toxicity prediction in 3D space and thus increase the explainability of the ML model. In summary, our findings offer promising insights considering 3D geometry information via EGNNs and provide a straightforward way to integrate molecular conformers into ML-based pipelines for predicting and investigating toxicity prediction in physical space. We expect that in the future, especially for larger, more diverse data sets, EGNNs will be an essential tool in this domain.

PAPER

https://pubs.acs.org/doi/full/10.1021/acs.chemrestox.3c00032

CODE and MODELS:

The conformer data sets and trained toxicity models will be published upon acceptance of this work. The code has been made available at https://github.com/jule-c/ET-Tox, and the processed data as well as pretrained models for training and testing can be downloaded from https://zenodo.org/record/7942946. We can provide the full list of conformers as XYZ files upon request.
DOI: 10.5281/zenodo.11237635
title: Conformer datasets for "Equivariant Graph Neural Networks for Toxicity Prediction"

description: Predictive modeling of toxicity is a crucial step in the drug discovery pipeline. It can help filter out molecules with a high probability of failing in the early stages of de novo drug design. Thus, several machine learning (ML) models have been developed to predict the toxicity of molecules by combining classical ML techniques or deep neural networks with well-known molecular representations such as fingerprints or 2D graphs. But the more natural, accurate representation of molecules is expected to be defined in physical 3D space like in ab initio methods. Recent studies successfully used equivariant graph neural networks (EGNNs) for representation learning based on 3D structures to predict quantum-mechanical properties of molecules. Inspired by this, we investigated the performance of EGNNs to construct reliable ML models for toxicity prediction. We used the equivariant transformer (ET) model in TorchMD-NET for this. Eleven toxicity data sets taken from MoleculeNet, TDCommons, and ToxBenchmark have been considered to evaluate the capability of ET for toxicity prediction. Our results show that ET adequately learns 3D representations of molecules that can successfully correlate with toxicity activity, achieving good accuracies on most data sets comparable to state-of-the-art models. We also test a physicochemical property, namely, the total energy of a molecule, to inform the toxicity prediction with a physical prior. However, our work suggests that these two properties can not be related. We also provide an attention weight analysis for helping to understand the toxicity prediction in 3D space and thus increase the explainability of the ML model. In summary, our findings offer promising insights considering 3D geometry information via EGNNs and provide a straightforward way to integrate molecular conformers into ML-based pipelines for predicting and investigating toxicity prediction in physical space. We expect that in the future, especially for larger, more diverse data sets, EGNNs will be an essential tool in this domain.

PAPER

https://pubs.acs.org/doi/full/10.1021/acs.chemrestox.3c00032

CODE and MODELS:

The conformer data sets and trained toxicity models will be published upon acceptance of this work. The code has been made available at https://github.com/jule-c/ET-Tox, and the processed data as well as pretrained models for training and testing can be downloaded from https://zenodo.org/record/7942946. We can provide the full list of conformers as XYZ files upon request.
DOI: 10.3886/e171321
title: Data and Code for: Optimality of Matched-Pair Designs in Randomized Controlled Trials

description: In randomized controlled trials (RCTs), treatment is often assigned by stratified randomization. I show that among all stratified randomization schemes which treat all units with probability one half, a certain matched-pair design achieves the maximum statistical precision for estimating the average treatment effect (ATE). In an important special case, the optimal design pairs units according to the baseline outcome. In a simulation study based on datasets from 10 RCTs, this design lowers the standard error for the estimator of the ATE by 10% on average, and by up to 34%, relative to the original designs.
DOI: 10.3886/e171321v1
title: Data and Code for: Optimality of Matched-Pair Designs in Randomized Controlled Trials

description: In randomized controlled trials (RCTs), treatment is often assigned by stratified randomization. I show that among all stratified randomization schemes which treat all units with probability one half, a certain matched-pair design achieves the maximum statistical precision for estimating the average treatment effect (ATE). In an important special case, the optimal design pairs units according to the baseline outcome. In a simulation study based on datasets from 10 RCTs, this design lowers the standard error for the estimator of the ATE by 10% on average, and by up to 34%, relative to the original designs.
DOI: 10.3886/e171321v2
title: Data and Code for: Optimality of Matched-Pair Designs in Randomized Controlled Trials

description: In randomized controlled trials (RCTs), treatment is often assigned by stratified randomization. I show that among all stratified randomization schemes which treat all units with probability one half, a certain matched-pair design achieves the maximum statistical precision for estimating the average treatment effect (ATE). In an important special case, the optimal design pairs units according to the baseline outcome. In a simulation study based on datasets from 10 RCTs, this design lowers the standard error for the estimator of the ATE by 10% on average, and by up to 34%, relative to the original designs.
DOI: 10.15468/dl.v6zb4k
title: Occurrence Download

description: A dataset containing 68802 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Cenchrus americanus (L.) Morrone)"
 ]
}

 The dataset includes 68802 records from 506 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027511-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.346xnq
title: Occurrence Download

description: A dataset containing 3758 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Eragrostis tenuifolia (A.Rich.) Hochst. ex Steud.)"
 ]
}

 The dataset includes 3758 records from 201 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027600-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3cjpb8
title: Occurrence Download

description: A dataset containing 22287 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Hordeum marinum Huds.)"
 ]
}

 The dataset includes 22287 records from 484 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027605-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbkrw4
title: Occurrence Download

description: A dataset containing 6622 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Solanum diphyllum L.)"
 ]
}

 The dataset includes 6622 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027611-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2hn79q
title: CCDC 2313353: Experimental Crystal Structure Determination

description: Related Article: Xiang-Yue Qi, Xiu-Zhen Li, Xi-Hui Diao, Yaseen Muhammad, Chao Chen, Hao Wang, Chuan-Song Qi, Wei Li, Ye Hong|2024|Inorg.Chim.Acta|569|122128|doi:10.1016/j.ica.2024.122128
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.epkhst
title: Occurrence Download

description: A dataset containing 13809 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Cyperus iria L.)"
 ]
}

 The dataset includes 13809 records from 484 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027601-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qvdmwr
title: Occurrence Download

description: A dataset containing 1087 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Silene viscosa (L.) Pers."
 ]
}

 The dataset includes 1087 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092642-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g7x3mg
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "IucnRedListCategory is EN",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0432961-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qqkx6a
title: Occurrence Download

description: A dataset containing 3419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myriophyllum verticillatum L.",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 3419 records from 181 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092684-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pu9ka2
title: Occurrence Download

description: A dataset containing 2590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Linyphia hortensis Sundevall, 1830)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 2590 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244555-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pr7yrs
title: Occurrence Download

description: A dataset containing 5041 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Country is one of (United States of America, Mexico, Canada)",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Icterus wagleri P.L.Sclater, 1857"
 ]
}

 The dataset includes 5041 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092663-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.