cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/fvd-080-a93
title: Pimpinella saxifraga L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0020176.10fu
title: SH0020176.10FU

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: 10.3535/a4j-sl4-zqx
title: Pimpinella saxifraga L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/kz8-rhw-xp4
title: Viola selkirkii Pursh ex Goldie

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0020177.10fu
title: SH0020177.10FU

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: 10.3535/par-h1k-zql
title: Pimpinella saxifraga L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0020178.10fu
title: SH0020178.10FU

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: 10.3535/254-rgq-zac
title: Pimpinella saxifraga L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/lbe-rc1-m60
title: Pimpinella saxifraga L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0020179.10fu
title: SH0020179.10FU

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: 10.15468/dl.4sgbd2
title: Occurrence Download

description: A dataset containing 879 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abutilon abutiloides (Jacq.) Garcke",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 879 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000787-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6tsy4
title: Occurrence Download

description: A dataset containing 1640 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abelia chinensis R.Br.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1640 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000784-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kweg2a
title: Occurrence Download

description: A dataset containing 729 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abutilon palmeri A.Gray",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 729 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000791-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14917319
title: RIME: Model Weights and Dataset for Predicting RNA-RNA Interactions

description: RIME is a deep learning model designed for predicting RNA-RNA interactions. This Zenodo repository contains the model weights and the dataset used for training and evaluation. Please 

If this source code is helpful for your research, please cite the following publication:

"Decoding RNA-RNA Interactions: The Role of Low-Complexity Repeats and a Deep Learning Framework for Sequence-Based Prediction"

Adriano Setti†, Giorgio Bini†, Valentino Maiorca, Flaminia Pellegrini, Gabriele Proietti, Dimitrios Miltiadis-Vrachnos, Alexandros Armaos, Julie Martone, Michele Monti, Giancarlo Ruocco, Emanuele Rodolà, Irene Bozzoni, Alessio Colantoni*, Gian Gaetano Tartaglia*

†Co-first authors *Corresponding authors

This model and dataset are described in our preprint:https://www.biorxiv.org/content/10.1101/2025.02.16.638500v1
DOI: 10.15468/dl.7dz4me
title: Occurrence Download

description: A dataset containing 5509820 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 5509820 records from 890 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000769-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2b3n99
title: Occurrence Download

description: A dataset containing 1389 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Dioscorea hispida Dennst."
 ]
}

 The dataset includes 1389 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000794-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k2tgxm
title: Occurrence Download

description: A dataset containing 138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is January",
 "OccurrenceStatus is Present",
 "TaxonKey is Ornithorhynchus anatinus (Shaw, 1799)",
 "Year 2024-2025"
 ]
}

 The dataset includes 138 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000795-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tux8y8
title: Occurrence Download

description: A dataset containing 14724 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Abelia chinensis R.Br., Abronia villosa S.Watson, Abutilon abutiloides (Jacq.) Garcke, Abutilon indicum (L.) Sweet, Abutilon palmeri A.Gray, Acaena splendens Hook. & Arn., Acalypha californica Benth., Acantholimon lycopodioides (Girard) Boiss., Acanthophyllum sedifolium (Kurz) Madhani & Zarre, Acanthoprasium integrifolium (Benth.) Ryding)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 14724 records from 316 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000793-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vr3vfk
title: Occurrence Download

description: A dataset containing 437 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Senegal",
 "TaxonKey is one of (Charadrius alexandrinus Linnaeus, 1758, Charadrius alexandrinus nivosus (Cassin, 1858), Charadrius alexandrinus dealbatus (Swinhoe, 1870), Charadrius alexandrinus tenuirostris Lawrence, 1862)"
 ]
}

 The dataset includes 437 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000792-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60707/ht34-5997
title: 40Ar/39Ar geochronology and thermochronology
DOI: 10.18462/iir.icr.2019.1296
title: Comparing open and closed vertical refrigerated display cabinets at mild and tropical external environments.
DOI: 10.13026/c28c71
title: The PTB Diagnostic ECG Database

description: The ECGs in this collection were obtained using a non-commercial, PTB prototype recorder with the following specifications:
16 input channels, (14 for ECGs, 1 for respiration, 1 for line voltage); Input voltage: ±16 mV, compensated offset voltage up to ± 300 mV
Input resistance: 100 Ω (DC);  Resolution: 16 bit with 0.5 μV/LSB (2000 A/D units per mV);  Bandwidth: 0 - 1 kHz (synchronous sampling of all channels);  Noise voltage: max. 10 μV (pp), respectively 3 μV (RMS) with input short circuit;  Online recording of skin resistance; Noise level recording during signal collection. The database contains 549 records from 290 subjects (aged 17 to 87, mean 57.2; 209 men, mean age 55.5, and 81 women, mean age 61.6; ages were not recorded for 1 female and 14 male subjects). Each subject is represented by one to five records.
DOI: 10.24381/cds.bce175f0
title: Global bioclimatic indicators from 1979 to 2018 derived from reanalysis
DOI: 10.5281/zenodo.11504576
title: Coupling a high-Q resonator to a spin qubit with all-electrical control

description: Supplementary data for:

"Coupling a high-Q resonator to a spin qubit with all-electrical control"

Rafael S. Eggli, Taras Patlatiuk, Eoin G. Kelly, Alexei Orekhov, Gian Salis, Richard J. Warburton, Dominik M. Zumbühl, Andreas V. Kuhlmann
DOI: 10.6073/pasta/7f1dac6bf350221c54d1eb349ca89bbf
title: Carbon decomposition and nitrogen mineralization in Marsden agroecosystem diversification experiment, Iowa, 2021

description: This dataset contains measurements of soil carbon decomposition and nitrogen mineralization from 36 soils in the Marsden agroecosystem diversification experiment. Soil samples were collected in fall 2021 from a long-term experiment initiated in 2002 at Iowa State University's Marsden Farm. The dataset includes laboratory data on soil organic carbon (SOC) content, soil total nitrogen content, the carbon-to-nitrogen ratio of soil, time-series CO2 fluxes from SOC decomposition in a 13.5-month lab incubation, and soil nitrogen mineralization rates. It also provides model simulations of SOC decomposition from different carbon pools using three process-based models: the Agricultural version of the Integrated Biosphere Simulator (Agro-IBIS), CN-SIM, and the Microbial-ENzyme Decomposition (MEND) models.
DOI: 10.60707/9kzh-1k32
title: 40Ar/39Ar geochronology and thermochronology
DOI: 10.25318/9810061801-eng
title: Mother tongue by immigrant status and period of immigration and number of languages known: Canada, provinces and territories, census metropolitan areas and census agglomerations with parts

description: Data on mother tongue by immigrant status and period of immigration, number of languages known, age and gender for the population in private households in Canada, provinces and territories, census metropolitan areas and census agglomerations with parts.
DOI: 10.25375/uct.14972463.v1
title: Characterisation of sulfide-enriched fine coal waste

description: This data set aims to estimate the characteristics of a sulfide-enriched fine coal waste stream that was obtained using a multi-stage separation process for the purpose of early-stage design alternative identification, selection and evaluation.
DOI: 10.34724/casd.65.4173.v1
title: Pratiques culturales en viticulture - 2019

description: L’enquête sur les pratiques culturales des viticulteurs a été réalisée pour la première fois en 2006 dans le cadre d’une convention conclue entre le ministère de l’Agriculture et de la Pêche, Viniflhor et l’Ifen. Elle complète les enquêtes réalisées sur les grandes cultures. Elle constitue un outil majeur de description des pratiques des viticulteurs.
DOI: 10.5281/zenodo.10635080
title: Autophagy regulator ATG5 maintains cerebellar function by preventing its excessive glycolytic activity.

description: The uploaded metabolomic dataset contains liquid-chromatography-mass spectrometry (LC-MS) data associated to the publication of Janine Tutas et al. from the Natalia Kononenko laboratory. 

The title of the publication is:

Autophagy regulator ATG5 preserves cerebellar function by safeguarding its glycolytic activity.

This article is to be published in Nature Metabolism 

Article Abstract

Dysfunctions in autophagy, a cellular mechanism for breaking down components within lysosomes, often lead to neurodegeneration. The specific mechanisms underlying neuronal vulnerability to autophagy dysfunction remain elusive. Here, we show that autophagy contributes to the survival of cerebellar Purkinje cells (PCs) by safeguarding their glycolytic activity. This function of autophagy is independent of its conventional housekeeping role and involves ATG5-mediated regulation of glucose transporter 2 (GLUT2) levels during cerebellar maturation. Autophagy-deficient PCs exhibit GLUT2 accumulation on the plasma membrane, along with increased glucose uptake and alterations in glycolysis. We identify lysophosphatidic acid and serine as glycolytic intermediates that trigger PC death and demonstrate that deletion of GLUT2 in ATG5-deficient mice mitigates PC neurodegeneration and restores their ataxic gait. Taken together, this work reveals a novel mechanism for regulating GLUT2 levels in neurons and provides new insights into the neuroprotective role of autophagy by controlling glucose homeostasis in the brain.
DOI: 10.5281/zenodo.11093937
title: Supporting data for publication: The role of the three-dimensional geometry of fault steps on event migration during fluid-induced seismic sequences.

description: This repository contains the supplementary data used in the publication Roche et al., 2024 (The role of the three-dimensional geometry of fault steps on event migration during fluid-induced seismic sequences), including (1) the seismicity catalogues from Cahuilla, Yellowstone and West Bohemia, modified from Ross et al. (2020), Shelly et al. (2013) and Hainzl et al. (2016), and (2) the pictures series used to build isochrone contour maps.

1.     Seismicity catalogues

The seismicity catalogues from Cahuilla, Yellowstone and West Bohemia are modified from Ross et al. (2020), Shelly et al. (2013) and Hainzl et al. (2016). The catalogues include the hypocentre location, relative time, and magnitude for non-filtered and filtered data. General information on each catalogue and filtering and modifications can be found in the associated publication.

 Dataset list:



Cahuilla Catalogues (modified from Ross et al., 2019): 



Original data: File name: VR_sup_0021_Cah_All

Filtered data: File name: VR_sup_0022_Cah_Filter


Bohemia 2008 Catalogues (modified from Haintzl et al., 2016): 



Original data: File name: VR_sup_0023_Boh_08_All

Filtered data: File name: VR_sup_0024_Boh_08_Filter


Bohemia 2014 Catalogues (modified from Haintzl et al., 2016): 



Original data: File name: VR_sup_0025_Boh_14_All

Filtered data: File name: VR_sup_0026_Boh_14_Filter


Yellowstone Catalogs (modified from Shelly et al., 2013): 



Original data: File name: VR_sup_0027_Yell_14_All

Filtered data: File name: VR_sup_0028_Yell_14_Filter



The files are text files tab-delimited, with the following headers:



Index: 1 by default

Easting(m): hypocenter Easting in meters 

Northing(m): hypocenter Northing in meters 

Depth(m): hypocenter depth in meters 

Mw: magnitude

Relative Time(s): date of the origin time in the format 


2.     Seismicity catalogues

The pictures series are images of seismicity at a regular time interval for each studied step.

Dataset list:



Step C1: File name: VR-sup-0012-Pictures_C1.

Step C2: File name: VR-sup-0013-Pictures_C2.

Step C3: File name: VR-sup-0014-Pictures_C3.

Step C4: File name: VR-sup-0015-Pictures_C4.

Step Y1: File name: VR-sup-0016-Pictures _Y1.

Step B1I: File name: VR-sup-0017-Pictures _B1I.

Step B1II: File name: VR-sup-0018-Pictures _B1II.

Step B2: File name: VR-sup-0019-Pictures _B2.

Step B3: File name: VR-sup-0020-Pictures _B3.


Each file contains a series of pictures in JPEG format. For each picture, events in the overlying and underlying segments are indicated in blue and red. The full circles represent the events occurring during the last interval. The empty circles represent the events occurring in the previous intervals.

If you find these data useful in your research, please cite Roche et al. (2024), as well as the relevant papers Ross et al. (2020), Shelly et al. (2013) and Hainzl et al. (2016).
DOI: 10.5281/zenodo.1172783
title: Silva Taxonomic Training Data Formatted For Dada2 (Silva Version 132)

description: These DADA2-formatted training fasta files were derived from the Silva Project's version 132 release. They are available under the Silva dual-licensing model for academia and commercial users: https://www.arb-silva.de/silva-license-information/

These fastas were generated by the following commands (using the dada2 R package version 1.7.6):


path &lt;- "~/Desktop/Silva/Silva.nr_v132"<br>
dada2:::makeTaxonomyFasta_Silva(file.path(path, "silva.nr_v132.align"), file.path(path, "silva.nr_v132.tax"), "~/tax/silva_nr_v132_train_set.fa.gz")

dada2:::makeSpeciesFasta_Silva("~/Desktop/Silva/SILVA_132_SSURef_tax_silva.fasta.gz", "~/tax/silva_species_assignment_v132.fa.gz")
DOI: 10.5281/zenodo.1447330
title: Silva V128 And V132 Dada2 Formatted 18S 'Train Sets'

description: These are species-level taxonomy classification training sets for the assignTaxonomy function from the dada2 R package.

The v132 training set includes every Eukaryotic organism from SILVA's v132 database, clustered at 99% similarity.

The v128 training set includes every Eukaryotic organism from SILVA's v128 database, clustered at 99% similarity. Additionally, it includes corrected species labels for the Blastocystis clade, and 37 Entamoeba sequences sourced from GenBank not present in the original v128 db. The v128 training set is modified specifically to allow for better species-level assignments for those two clades in mammalian gut microbiome studies.
DOI: 10.6141/tw-srda-ae080006-1
title: 2019 Mobile Phone Users' Digital Opportunity Survey

description: Mobile Phone Users' Digital Opportunity Survey
DOI: 10.5281/zenodo.3737112
title: Synthetic metagenome

description: Synthetic metagenome generated with randomreads.sh from the BBMap package (v38.79). Five bacterial genome assemblies were downloaded from NCBI: <strong>name;genome_id;taxid</strong><br> Thermoplasmatales archaeon I-plasma;GCA_009387875;667138<br> Patulibacter medicamentivorans;GCF_000240225;1097667<br> Lachnospiraceae bacterium 2_1_46FAA;GCA_000209385;742723<br> Enterobacteriaceae bacterium LSJC7;GCA_000302695;1224136<br> Burkholderia mallei 2002721280;GCF_000011705;370895 200,000 paired reads were generated from each genome by running: <pre><code class="language-bash">randomreads.sh ref=&lt;genome&gt;.fna out1=&lt;genome&gt;_1.fq out2=&lt;genome&gt;_2.fq reads=200000 paired=t illuminanames=t prefix=&lt;taxid&gt; </code></pre> The two paired fastq files were concatenated and gzipped separately.
DOI: 10.15468/dl.q22y5t
title: Occurrence Download

description: A dataset containing 1722174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "Year is 2010",
 "Month is September"
 ]
}

 The dataset includes 1722174 records from 493 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000776-250225214225278/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fnfa44
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Integrated Taxonomic Information System (ITIS)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011053-250402121839773/datasets/export for details.