cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.2vnbw7
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-89.77816 14.08462,-88.72734 14.07534,-88.68098 14.89437,-89.7318 14.91291,-89.77816 14.08462))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dasyprocta punctata Gray, 1842"
 ]
}

 The dataset includes 42 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018831-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s2268m
title: Occurrence Download

description: A dataset containing 433 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydrolycus armatus (Jardine, 1841)"
 ]
}

 The dataset includes 433 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018830-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15472/iy6xxr
title: Colección Taxonómica Central del museo entomológico UNAB, familia Coccinellidae

description: El Museo Entomológico UNAB contiene cerca de 180.000 especímenes, con las siguientes características de conservación: 153.000 montados en alfiler y almacenados en 980 gavetas de madera tipo Cornell, ubicadas en seis paneles de compactadores y 395 cajas misceláneas en estanterías; 10.430 montadas en láminas: Coccomorpha (6.600 láminas), Collembola (1.700), Aphidomorpha (1400), Aleyrodomorpha (500), Thysanoptera (90), Acari (90), Psyllomorpha (50); 18.400 entre larvas y adultos, envasados en 4.600 frascos con alcohol, y 96 especímenes tipo montados en alfiler, que representan 46 especies. Aproximadamente, 20.000 especímenes se encuentran catalogados en la base digital de la Colección Taxonómica Central (CTC) del Museo UNAB, 17.000 de los cuales se encuentran identificados por especialistas, a nivel de género o especie. Dichas identificaciones representan un total de 4.000 especies, en 150 familias y 19 órdenes de insectos; así como siete especies de Acari en dos familias.
description: En el presente recuso se documentan 28 registros biológicos pertenecientes a 4 géneros y 2 especies de la familia Coccinellidae recolectados entre 2014 y 2024 en Caquetá, Guaviare y Putumayo, Colombia. Todos los registros se encuentran actualmente depositados en el museo entomológico UNAB, de la Facultad de Ciencias Agrarias de la Universidad Nacional de Colombia, sede Bogotá.
DOI: 10.15468/dl.ptjxf6
title: Occurrence Download

description: A dataset containing 36448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Streptomyces Waksman & Henrici, 1943"
 ]
}

 The dataset includes 36448 records from 425 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018827-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bd9zx6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "ScientificName" : [
 "is one of (historis odius)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018832-250525065834625/datasets/export for details.
DOI: 10.15468/dl.dxecmm
title: Occurrence Download

description: A dataset containing 56453 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Boletus edulis Bull.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 56453 records from 278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018813-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vzr3jn
title: Occurrence Download

description: A dataset containing 2486491 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "StateProvince is British Columbia",
 "DatasetKey is iNaturalist Research-grade Observations"
 ]
}

 The dataset includes 2486491 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018821-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wdj28e
title: Occurrence Download

description: A dataset containing 4352 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Historis odius (Fabricius, 1775)"
 ]
}

 The dataset includes 4352 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018833-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/12051629
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.m8bcwe
title: Occurrence Download

description: A dataset containing 56453 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Boletus edulis Bull.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 56453 records from 278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018817-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15567577
title: Social Network Data for Jones, Bonacich Centrality and Relational Social Networks at the Highest Levels of the Assyrian Government during the Reign of Sargon II (722-705 BC)

description: Social network data from the reign of Sargon II.
DOI: 10.5281/zenodo.15567578
title: Social Network Data for Jones, Bonacich Centrality and Relational Social Networks at the Highest Levels of the Assyrian Government during the Reign of Sargon II (722-705 BC)

description: Social network data from the reign of Sargon II.
DOI: 10.5281/zenodo.15572350
title: Social Network Data for Jones, Bonacich Centrality and Relational Social Networks at the Highest Levels of the Assyrian Government during the Reign of Sargon II (722-705 BC)

description: Social network data from the reign of Sargon II.
DOI: 10.15468/dl.6zgdq9
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Nepal, Bhutan, Bangladesh, Pakistan, China, India, Myanmar, Afghanistan)",
 "TaxonKey is Celaenorrhinus putra (Moore, 1865)"
 ]
}

 The dataset includes 53 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022393-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tb5bf9
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia affinis (Baird & Girard, 1853)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -28.5786,20.509 -28.5786,20.509 -32.9007,25.5395 -32.9007,25.5395 -28.5786))"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022394-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j6mn6j
title: Occurrence Download

description: A dataset containing 22597 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crypturellus parvirostris"
 ]
}

 The dataset includes 22597 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025654-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/cdc.366
title: Chandra X-ray Observatory Chandra Data Collection for request #366

description: Chandra Data Collection for request #366
description: DOI updated to include the publication's DOI on 2025-08-20-10:00:00
DOI: 10.5281/zenodo.16904959
title: Dataset: Unveiling Earthquakes:  Thermoluminescence Signal Resetting of Laboratory-Produced Fault Gouge

description: # Data Structure

 

## 00_MeasurementData

 

This folder contains the original unmodified measurements data, i.e. measurement

sequence files (.lseq) and output (.xsyg). Data from experiments

are organised in separate folders. 

 

## 10_AnalysisScripts

 

This folder contains the R scripts used to analyse the data. 

Please note that you have to modified file paths in order to re-run 

the scripts. 

 

## 20_Output

 

The processed measurement output data as CSV, PDF, PNG or GIF.

This output is intermediate and final measurement data output.

 

 

# Additional note

 

The samples had different names during the preparation and

measurement and these names were modified for better readability 

and consistency during manuscript preparation. 

 

 






ORIGNAL_NAME
NAME_IN_MANUSCRIPT


Standard75Gy
SM


FGB
FGBA


FGC
FGC


MS
MMAB
DOI: 10.5281/zenodo.16904960
title: Dataset: Unveiling Earthquakes:  Thermoluminescence Signal Resetting of Laboratory-Produced Fault Gouge

description: # Data Structure

 

## 00_MeasurementData

 

This folder contains the original unmodified measurements data, i.e. measurement

sequence files (.lseq) and output (.xsyg). Data from experiments

are organised in separate folders. 

 

## 10_AnalysisScripts

 

This folder contains the R scripts used to analyse the data. 

Please note that you have to modified file paths in order to re-run 

the scripts. 

 

## 20_Output

 

The processed measurement output data as CSV, PDF, PNG or GIF.

This output is intermediate and final measurement data output.

 

 

# Additional note

 

The samples had different names during the preparation and

measurement and these names were modified for better readability 

and consistency during manuscript preparation. 

 

 






ORIGNAL_NAME
NAME_IN_MANUSCRIPT


Standard75Gy
SM


FGB
FGBA


FGC
FGC


MS
MMAB
DOI: 10.5281/zenodo.16911767
title: Patterns and environmental drivers of soil microbial succession

description: Succession has been a central theme of ecology for over a century, yet the patterns and drivers of soil microbial succession remain less well understood. Here, we analyzed the raw sequencing data of 5184 soil samples involving microbial succession, including primary succession, forest and grassland secondary succession. We provide the first evidence that the β-diversity (β-total, compositional dissimilarity between communities) of soil bacterial and fungal communities both decreased significantly with successional age in the three successional types. This indicates that convergent succession (i.e., decrease in β-total with time) is prevalent and independent of successional types and initial conditions. Partitioning β-total into species addition and replacement revealed that species addition dominates in early succession and then declines with successional age, whereas species replacement shows an increasing pattern over succession and ultimately dominates the late-successional communities. The convergent succession is mainly attributed to the directional species replacement and is driven by the changes in soil properties. In primary succession, β-total in bacterial communities is negatively correlated with soil total nitrogen (TN), soil organic carbon (SOC), NO₃⁻-N, and NH₄⁺-N, and β-total in fungal communities is negatively related to soil TN, NH₄⁺-N, and NO₃⁻-N. In forest secondary succession, β-total in bacterial communities is negatively correlated with TN and SOC, and β-total in fungal communities is negatively related to TN, SOC, and NH₄⁺-N. In grassland secondary succession, β-total in bacterial communities is positively associated with the changes in soil pH (ΔpH), and β-total in fungal communities is negatively related to TN and SOC. Except for grassland bacterial succession, soil microbial communities generally shift from r-strategy (copiotrophs) to K-strategy (oligotrophs) during succession. Basidiomycota and ectomycorrhizal fungi display a consistent increasing trend over time in the three successional types. Together, our study fills the knowledge gap in soil microbial succession patterns and highlights the universality of community convergence as predicted by the classical macro-ecological model.
DOI: 10.15468/dl.kqzqxm
title: Occurrence Download

description: A dataset containing 345 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oreochromis mossambicus (Peters, 1852)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.5701 -24.0715,25.5395 -24.0715,25.5395 -28.5786,30.5701 -28.5786,30.5701 -24.0715))"
 ]
}

 The dataset includes 345 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022105-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15572179
title: LeafMachine2 Data: Hydrangeaceae Leaf Outlines and ECT

description: Hydrangeaceae - 213,607 leaves - 27.8 GB: This repository contains HDF5 (.h5) files with leaf morphological data for species in the Hydrangeaceae family. Each file represents a single leaf specimen and contains leaf shape outlines, the 128x128 ECT matrix, and associated metadata.

File Contents

This dataset contains 213,607 leaves from taxa in the family Hydrangeaceae. Some leaves may be partial, predated, broken, or incomplete. Each .h5 file contains the following datasets:



ECT_matrices/ - Euler Characteristic Transform (ECT) matrices capturing topological features of leaf shapes

shapes/shape_0 - Coordinate array (x,y) defining the leaf outline boundary

component_names - Original filename identifier (without extension)

group_labels - Taxonomic classification dictionary containing:



family: Taxonomic family name

genus: Genus classification

genus_species: Binomial species name

fullname: Complete taxonomic identifier




Data Format

Files are organized with standardized naming: [Herbarium]_[ID]_[Family]_[Genus]_[Species]__[LeafID].h5 Shape coordinates are normalized to a unit circle centered at the origin (-0.5 to 0.5 range), vertically oriented.

Uncompressed Size

27.8 GB

Usage

Code for reading, processing, and analyzing these files is available at: https://github.com/Gene-Weaver/LM2-Data-Tools The repository includes functions for extracting data and generating visualizations.

Citation

Please cite the LeafMachine2 paper and this dataset.

Weaver, W. N., & Smith, S. A. (2023). From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2. Applications in Plant Sciences, 11(5), e11548. https://doi.org/10.1002/aps3.11548
DOI: 10.5281/zenodo.15572180
title: LeafMachine2 Data: Hydrangeaceae Leaf Outlines and ECT

description: Hydrangeaceae - 213,607 leaves - 27.8 GB: This repository contains HDF5 (.h5) files with leaf morphological data for species in the Hydrangeaceae family. Each file represents a single leaf specimen and contains leaf shape outlines, the 128x128 ECT matrix, and associated metadata.

File Contents

This dataset contains 213,607 leaves from taxa in the family Hydrangeaceae. Some leaves may be partial, predated, broken, or incomplete. Each .h5 file contains the following datasets:



ECT_matrices/ - Euler Characteristic Transform (ECT) matrices capturing topological features of leaf shapes

shapes/shape_0 - Coordinate array (x,y) defining the leaf outline boundary

component_names - Original filename identifier (without extension)

group_labels - Taxonomic classification dictionary containing:



family: Taxonomic family name

genus: Genus classification

genus_species: Binomial species name

fullname: Complete taxonomic identifier




Data Format

Files are organized with standardized naming: [Herbarium]_[ID]_[Family]_[Genus]_[Species]__[LeafID].h5 Shape coordinates are normalized to a unit circle centered at the origin (-0.5 to 0.5 range), vertically oriented.

Uncompressed Size

27.8 GB

Usage

Code for reading, processing, and analyzing these files is available at: https://github.com/Gene-Weaver/LM2-Data-Tools The repository includes functions for extracting data and generating visualizations.

Citation

Please cite the LeafMachine2 paper and this dataset.

Weaver, W. N., & Smith, S. A. (2023). From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2. Applications in Plant Sciences, 11(5), e11548. https://doi.org/10.1002/aps3.11548
DOI: 10.6084/m9.figshare.28563854.v2
title: deconvMe data

description: We generated sample-matched readouts from PBMCs of chronic Hepatitis C virus-infected patients for DNAm using Illumina EPIC arrays, gene expression using RNA-seq, and proportions of selected immune cells using flow cytometry. This repository contains the processed TPM and count matrices for RNAseq, the beta matrix and two matrices quantifying the methylated and unmethylated probes, and a metadata table that gives information on sample IDs, gender, and flow-cytometry-derived immune cell-type fractions:<br>RNA-seq:tpm.csvcounts.csvDNAm:meth.csvunmeth.csvbeta.csvmetadata + flow cytometry:meta_flow.csv<br><br>Raw <i>fastq</i> files from the RNA sequencing have been processed using the nf-core rnaseq pipeline version 3.10. The main steps include a manual inspection of quality using <i>FastQC</i>, followed by pseudo-alignment and gene quantification using <i>Salmon</i>. Next to raw gene expression counts, this method generates transcript per million (TPM) counts, which are normalized by gene length and library size and were used as input for deconvolution methods.DNAm data by Illumina EPIC arrays generated raw <i>idat</i> files that have been processed with <i>RnBeads</i> 2.0 using the default settings during preprocessing, which removes methylation sites with too many missing values, cross-reactive probes, or those that overlap with known single-nucleotide polymorphisms (SPNs). Additionally, we removed all CpGs with NA values in any sample. The final dataset consisted of 724,082 CpGs. We removed CpGs located on sex chromosomes as they would confound the analysis.
DOI: 10.15468/dl.f6qu2d
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tanganicodus irsacae)",
 "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 21 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025202-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48544/69f2baa2-5717-472d-a05f-d4358900ad98
title: Navigating Music Technology
DOI: 10.15468/dl.f4rxqu
title: Occurrence Download

description: A dataset containing 2023 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paubrasilia echinata (Lam.) Gagnon, H.C.Lima & G.P.Lewis"
 ]
}

 The dataset includes 2023 records from 165 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022014-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h2js7h
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Labeo umbratus (Smith, 1841)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -28.5786,20.509 -28.5786,20.509 -32.9007,25.5395 -32.9007,25.5395 -28.5786))"
 ]
}

 The dataset includes 61 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022015-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15593254
title: African cichlid lake radiations recapitulate riverine axial morphologies through repeated exploration of morphospace

description: We present a dataset of vertebral counts, body shape measurements, and lateral radiographs for 4861 individuals representing 583 species of African cichlids. This comprehensive dataset captures the full range of axial phenotypic diversity across the group. Using phylogenetic comparative methods, we show that elongate, body plans supported by high vertebral counts, evolved in lacustrine cichlids as adaptations to pelagic, demersal, and piscivorous niches. In contrast, riverine species exhibit broader axial diversity, driven by higher rates of vertebral evolution. Axial morphospace occupancy correlates with the age of lake radiations, but divergence time alone does not explain the observed patterns. Our results suggest that axial diversity radiated outward from an ancestrally riverine morphology and underscore the utility of African cichlids as a model for studying vertebral evolution in teleosts. Please see the README.pdf file for full descriptions of each data file deposited here. Do not hesitate to contact me at callum.bucklow@biology.ox.ac.uk/c.v.bucklow@gmail.com for further information.
DOI: 10.5281/zenodo.15593255
title: African cichlid lake radiations recapitulate riverine axial morphologies through repeated exploration of morphospace

description: We present a dataset of vertebral counts, body shape measurements, and lateral radiographs for 4861 individuals representing 583 species of African cichlids. This comprehensive dataset captures the full range of axial phenotypic diversity across the group. Using phylogenetic comparative methods, we show that elongate, body plans supported by high vertebral counts, evolved in lacustrine cichlids as adaptations to pelagic, demersal, and piscivorous niches. In contrast, riverine species exhibit broader axial diversity, driven by higher rates of vertebral evolution. Axial morphospace occupancy correlates with the age of lake radiations, but divergence time alone does not explain the observed patterns. Our results suggest that axial diversity radiated outward from an ancestrally riverine morphology and underscore the utility of African cichlids as a model for studying vertebral evolution in teleosts. Please see the README.pdf file for full descriptions of each data file deposited here. Do not hesitate to contact me at callum.bucklow@biology.ox.ac.uk/c.v.bucklow@gmail.com for further information.
DOI: 10.5281/zenodo.15097002
title: Data related to the manuscript: Structural and mechanistic insights into the sequential dsDNA cleavage by SpCas12f1
DOI: 10.5281/zenodo.15097003
title: Data related to the manuscript: Structural and mechanistic insights into the sequential dsDNA cleavage by SpCas12f1