cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.88m7kt
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is Regroupement d'études et inventaires réalisés par la société BIOTOPE Sud-Ouest-Données de présence collectées sur les écrevisses",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 115 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0217477-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.px9far
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bryozoa",
 "DatasetKey is Données de l'association Perche Nature - Perche Nature - Inventaire de la Biodiversité Communale - 2019 - Epuisay / Mazange (41)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220872-230224095556074/datasets/export for details.
DOI: 10.15468/dl.bdzc6h
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salvia meiliensis S.W.Su"
 ]
}

 The dataset includes 15 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110065-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.waapad
title: Occurrence Download

description: A dataset containing 736 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sempervivum vicentei Pau"
 ]
}

 The dataset includes 736 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123044-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ac6hcd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bryozoa",
 "DatasetKey is Partenariats avec les Parcs Naturels Régionaux-Données CEN M-P partenariats PNR",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220882-230224095556074/datasets/export for details.
DOI: 10.15468/dl.jee7kj
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is Bibliographie de la faune, la flore et la fonge de France métropolitaine et outre-mer-Folia Conchyliologica [2010-]",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0217479-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rr57ez
title: Occurrence Download

description: A dataset containing 3098 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is SILENE-FAUNE-PACA - Parc_Naturel_Régional_du_Verdon_2017_12_18",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 3098 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0227039-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ysdh2
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Senecio abruptus Thunb."
 ]
}

 The dataset includes 220 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123056-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygapcs
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bryozoa",
 "DatasetKey is CardObs : Observations naturalistes issues de l'outil CardObs-EPTBSGL_ANSE_ARCOT_2019",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220873-230224095556074/datasets/export for details.
DOI: 10.15468/dl.msv3m6
title: Occurrence Download

description: A dataset containing 1002 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gamochaeta argyrinea G.L.Nesom"
 ]
}

 The dataset includes 1002 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0224099-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2u2fq
title: Occurrence Download

description: A dataset containing 1435 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ellochelon vaigiensis (Quoy & Gaimard, 1825)"
 ]
}

 The dataset includes 1435 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110066-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nputpf
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Geranium clarkei Yeo"
 ]
}

 The dataset includes 16 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0227042-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xhbaef
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fritillaria unibracteata P.K.Hsiao & K.C.Hsia"
 ]
}

 The dataset includes 91 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220875-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ntqjk
title: Occurrence Download

description: A dataset containing 13949 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is Système d'Information sur la Nature et les Paysages d'Ile de France - Données de la structure Naturessonne provenant de la base de donnée du SINP Île-de-France CETTIA",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 13949 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0217484-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x598an
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tachysurus sinensis Lacepède, 1803"
 ]
}

 The dataset includes 29 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110083-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kga6qf
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((123 -11,128 -11,128 -8,123 -8,123 -11))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Putranjivaceae"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0227043-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d5gzvu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bryozoa",
 "DatasetKey is Atlas de la Biodiversité Communales sur la Communauté de Commune de Montesquieu-Inventaire mollusques protocolé",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220883-230224095556074/datasets/export for details.
DOI: 10.15468/dl.mbsvyc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is Plateforme AUVERGNE-DREAL Auvergne-DREAL Auvergne - Autres - 2015",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0227477-230224095556074/datasets/export for details.
DOI: 10.15468/dl.mjpptw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bryozoa",
 "DatasetKey is Données de l'association Perche Nature - Perche Nature - Données publiques - 2019",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220877-230224095556074/datasets/export for details.
DOI: 10.15468/dl.fweuwx
title: Occurrence Download

description: A dataset containing 274 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is BoBO - Botanic Garden and Botanical Museum Berlin Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 274 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0217487-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mspv4x
title: Occurrence Download

description: A dataset containing 763 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osteomugil cunnesius (Valenciennes, 1836)"
 ]
}

 The dataset includes 763 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0110071-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e3t4z2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bryozoa",
 "DatasetKey is Données de l'association Indre Nature - Données Indre Nature 2020",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220878-230224095556074/datasets/export for details.
DOI: 10.15468/dl.834h25
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fimbristylis juncocephala Boeckeler"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0217489-230224095556074/datasets/export for details.
DOI: 10.15468/dl.r8x6ha
title: Occurrence Download

description: A dataset containing 1825 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arthropoda",
 "DatasetKey is Plan régional d'actions en faveur des odonates (PRAO) : 3ème phase (2017 - 2018) menée par le CEN Aquitaine-Observations faunistiques fortuites réalisées par le CEN Aquitaine (Étude Agrion de Mercure)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 1825 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0227056-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t284jd
title: Occurrence Download

description: A dataset containing 1094944 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Holcus lanatus L."
 ]
}

 The dataset includes 1094944 records from 2601 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028844-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kxpj24
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Passeriformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((120 80,130 80,130 90,120 90,120 80))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018607-251009101135966/datasets/export for details.
DOI: 10.34740/kaggle/dsv/13381464
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.6993123
title: Alanine dipeptide in an implicit solvent at 300K

description: This dataset has been introduced in the article Midgley, et al.: Flow Annealed Importance Sampling Bootstrap, 2022. It contains samples from the Boltzmann distribution of alanine dipeptide in an implicit solvent, which have been generated with a Replica Exchange Molecular Dynamics (REMD) simulation. The ff96 with an OBC GBSA implicit solvent was used. The REMD uses 21 replicas starting at a temperature of 300K and increasing the temperature by an increment of 50K. The replicas are exchanged every 200 iterations and use the state at each multiple of 1000 time steps as samples. Many of these simulations were in parallel with different seeds. We let the system equilibrate for \(2\times10^5\) iterations and run the simulation subsequently for \(2\times10^6\) iterations. The data is split into a training set, which consists of \(10^6\) samples; a validation set consisting of \(10^6\) samples as well; and a test set with \(10^7\) samples. The data is provided as raw \((x,y,z)\)-coordinates, stored as *.h5 files, and transformed to internal coordinates, stored as *.pt files. More details about the data and how to use it are given in our GitHub repository and paper.
DOI: 10.5281/zenodo.15526429
title: Molecular Dynamics of Alanine Dipeptide, Alanine Tetrapeptide, and Alanine Hexapeptide in Implicit Solvent

description: This repository contains the datasets used in our publication "Temperature-Annealed Boltzmann Generators" (https://arxiv.org/abs/2501.19077). See also our GitHub code repository that uses the provided datasets to evaluate trained Boltzmann generators (https://github.com/aimat-lab/TA-BG).

We provide training, evaluation, and test datasets subsampled from molecular dynamics trajectories performed in OpenMM with Amber force fields and implicit solvation. We cover the molecular systems alanine dipeptide, alanine tetrapeptide, and alanine hexapeptide. Coordinates are given in Cartesian coordinates in angstroms.

Details on simulation and force field parameters can be found in our publication.

Overview of the folder structure and files contained in datasets.zip:



aldp  -  Files for the alanine dipeptide system



300K_test_fab.npy  -  Test dataset at 300K, originally used in https://arxiv.org/abs/2208.01893 (Source: https://zenodo.org/records/6993124)

300K_train.npy  -  Training dataset at 300K, used for forward KLD experiments in our publication.

300K_val.npy  -  Validation dataset at 300K

1200K_val.npy  -  Validation dataset at 1200K






tetra  -  Files for the alanine tetrapeptide system



300K_test.npy  -  Test dataset at 300K

300K_train.npy  -  Training dataset at 300K, used for forward KLD experiments in our publication.

300K_val.npy  -  Validation dataset at 300K

1200K_val.npy  -  Validation dataset at 1200K






hexa  -  Files for the alanine hexapeptide system



300K_test.npy  -  Test dataset at 300K

300K_train.npy  -  Training dataset at 300K, used for forward KLD experiments in our publication.

300K_val.npy  -  Validation dataset at 300K

1200K_val.npy  -  Validation dataset at 1200K
DOI: 10.5281/zenodo.15526430
title: Molecular Dynamics of Alanine Dipeptide, Alanine Tetrapeptide, and Alanine Hexapeptide in Implicit Solvent

description: This repository contains the datasets used in our publication "Temperature-Annealed Boltzmann Generators" (https://arxiv.org/abs/2501.19077). See also our GitHub code repository that uses the provided datasets to evaluate trained Boltzmann generators (https://github.com/aimat-lab/TA-BG).

We provide training, evaluation, and test datasets subsampled from molecular dynamics trajectories performed in OpenMM with Amber force fields and implicit solvation. We cover the molecular systems alanine dipeptide, alanine tetrapeptide, and alanine hexapeptide. Coordinates are given in Cartesian coordinates in angstroms.

Details on simulation and force field parameters can be found in our publication.

Overview of the folder structure and files contained in datasets.zip:



aldp  -  Files for the alanine dipeptide system



300K_test_fab.npy  -  Test dataset at 300K, originally used in https://arxiv.org/abs/2208.01893 (Source: https://zenodo.org/records/6993124)

300K_train.npy  -  Training dataset at 300K, used for forward KLD experiments in our publication.

300K_val.npy  -  Validation dataset at 300K

1200K_val.npy  -  Validation dataset at 1200K






tetra  -  Files for the alanine tetrapeptide system



300K_test.npy  -  Test dataset at 300K

300K_train.npy  -  Training dataset at 300K, used for forward KLD experiments in our publication.

300K_val.npy  -  Validation dataset at 300K

1200K_val.npy  -  Validation dataset at 1200K






hexa  -  Files for the alanine hexapeptide system



300K_test.npy  -  Test dataset at 300K

300K_train.npy  -  Training dataset at 300K, used for forward KLD experiments in our publication.

300K_val.npy  -  Validation dataset at 300K

1200K_val.npy  -  Validation dataset at 1200K
DOI: 10.15156/bio/sh1406248.10fu
title: SH1406248.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1406250.10fu
title: SH1406250.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1406251.10fu
title: SH1406251.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.