cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1396915.10fu
title: SH1396915.10FU

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/sh1396918.10fu
title: SH1396918.10FU

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: 10.5281/zenodo.18741418
title: Tree cover in cocoa agroforestry: data and code

description: This repository provides the data and the Stan code for the model presented in “A Decision-Support Tool for Managing Tree-Cover in Smallholder Cocoa Agroforestry Systems.”

It contains two files:

1) data.csv: the dataset used to fit the model, with the following columns:

• site: site ID

• plot: plot number

• ba_ha: tree basal area (m² per hectare)

• n_ha: tree density (number of trees per hectare)

• cover: tree cover (between 0 and 1)

2) model.txt: the Stan model code.
DOI: 10.5281/zenodo.18741419
title: Tree cover in cocoa agroforestry: data and code

description: This repository provides the data and the Stan code for the model presented in “A Decision-Support Tool for Managing Tree-Cover in Smallholder Cocoa Agroforestry Systems.”

It contains two files:

1) data.csv: the dataset used to fit the model, with the following columns:

• site: site ID

• plot: plot number

• ba_ha: tree basal area (m² per hectare)

• n_ha: tree density (number of trees per hectare)

• cover: tree cover (between 0 and 1)

2) model.txt: the Stan model code.
DOI: 10.6084/m9.figshare.31375804.v1
title: Vertical Occipital Fasciculus (VOF) probability maps and ventral endpoints for pyAFQ

description: <br>Based off a combination of streamlines from the ORG atlas and endpoint regions from the AAL atlas. Please cite the associated papers below.<br><br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br><br>O'Donnell Research Group (ORG) Atlas<br>https://zenodo.org/records/2648292<br><br>Zhang, F., Wu, Y., Norton, I., Rathi, Y., Makris, N., O'Donnell, LJ. An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. NeuroImage, 2018 (179): 429-447<br><br>See details at: https://github.com/SlicerDMRI/ORG-Atlases<br><br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br><br>https://www.gin.cnrs.fr/en/tools/aal/<br><br>Automated anatomical labelling atlas 3. Rolls, E. T., Huang, C. C., Lin, C. P., Feng, J., & Joliot, M., <i>Neuroimage,</i><i> </i>2020, <i>206</i>, 116189, doi:10.1016/j.neuroimage.2019.116189Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas. Rolls ET, Joliot M & Tzourio-Mazoyer N. <i>NeuroImage</i> 2015, 122: 1-5.<br>http://dx.doi.org/10.1016/j.neuroimage.2015.07.075Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain. N. Tzourio-Mazoyer, B. Landeau, D. Papathanassiou, F. Crivello, O. Étard, N. Delcroix, B. Mazoyer, and M. Joliot. <i>NeuroImage</i> 2002, 15 :273-289<br>http://dx.doi.org/10.1006/nimg.2001.0978
DOI: 10.15468/dl.wns7uv
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "StateProvince is Wisconsin",
 "TaxonKey is Fragaria virginiana grayana"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003400-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frwa2v
title: Occurrence Download

description: A dataset containing 502 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "TaxonKey is Sciurus vulgaris",
 "Year 2026-2026"
 ]
}

 The dataset includes 502 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003402-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18741796
title: TransPharm SSbD sustainability score
DOI: 10.5281/zenodo.18741795
title: TransPharm SSbD sustainability score
DOI: 10.15468/dl.v75yd3
title: Occurrence Download

description: A dataset containing 388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is South Africa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is VU",
 "OccurrenceStatus is Present",
 "TaxonKey is Diomedea exulans",
 "Year 2006-2026"
 ]
}

 The dataset includes 388 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003406-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.epqakj
title: Occurrence Download

description: A dataset containing 39078 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((119.45035 32.5756,120.96869 32.5756,120.96869 34.46778,119.45035 34.46778,119.45035 32.5756))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves",
 "Year 2012-2021"
 ]
}

 The dataset includes 39078 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003401-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14501607
title: miRBench datasets

description: Changelog

The following listed datasets were recreated via a series of post-processing pipelines (available here) to eliminate a bias between the positive and negative classes (miRNA frequency class bias) discovered in previous versions of the datasets. All have a 1:1 positive to negative class ratio. 



AGO2_eCLIP_Manakov2022_leftout.tsv.gz

AGO2_eCLIP_Manakov2022_test.tsv.gz

AGO2_eCLIP_Manakov2022_train.tsv.gz

AGO2_eCLIP_Klimentova2022.tsv.gz

AGO2_CLASH_Hejret2023_test.tsv.gz

AGO2_CLASH_Hejret2023_train.tsv.gz


The structure of each dataset is consistent, with the following column order:



gene: A string of length 50 indicating the binding site sequence in the 5’ to 3’ direction.

noncodingRNA: A string of variable length (16–28) indicating the mature miRNA sequence in the 5’ to 3’ direction.

noncodingRNA_name: A string indicating the name of the miRNA.

noncodingRNA_fam: A string indicating the name of the miRNA family the miRNA belongs to.

feature: A string indicating the feature annotation on the genome where the binding site occurs.

label: A boolean value indicating whether the example belongs to the positive or negative class.

chr: A string indicating the chromosome number on the genome where the binding site occurs.

start: An integer indicating the 1-based start position of the binding site on the genome.

end: An integer indicating the 1-based end position of the binding site on the genome.

strand: A string indicating whether the binding site occurs on the ’+’ or ’-’ strand on the genome.

gene_cluster_ID: An integer indicating the cluster ID of the binding site sequence used to generate the negative class.


The following listed dataset is the concatenated HybriDetector output of all the selected samples from the available Manakov sample files. It therefore contains only a raw version of the positive class of the Manakov dataset. It is the input to the series of post-process pipelines for the Manakov dataset. 



AGO2_eCLIP_Manakov2022_full_dataset.tsv.gz


The other inputs to the post-process pipelines for the Hejret and Klimentova datasets are found at the following links. 



Hejret dataset

Klimentova dataset


Note that the binding sites reported in all datasets are consistent with GRCh38.
DOI: 10.15468/dl.eujykt
title: Occurrence Download

description: A dataset containing 48959 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Gadus morhua"
 ]
}

 The dataset includes 48959 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003403-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15125/bath-01608
title: Dataset for "Pioneering Net Zero Carbon Construction Policy in Bath & North East Somerset: Evaluating the effectiveness of novel planning policies over time"

description: This data was collected as part of a continuing collaboration between the University of Bath and Bath and North East Somerset Council, exploring the impacts of (and reception to) pioneering sustainable planning policies for new buildings which were first introduced in January 2023. This project evaluates the success of the policies two years on, establishing long-term trends, opportunities for refinement, and the national policy implications of this unique policy case study. 

The deposited data relates to two parts of the methodology. 

The first is an analysis of incoming planning application, relating to the characteristics of proposed buildings and key parameters submitted to comply with the net zero energy requirements.

The second is the results of a questionnaire sent out to applicants.
description: This dataset was generated through a mixed‑methods approach designed to capture both quantitative performance data and qualitative stakeholder perspectives relating to the B&NES sustainable construction policies. First, all eligible planning applications submitted between May 2024 and June 2025 were systematically reviewed. Energy summary data, SAP/PHPP modelling outputs and associated documentation were extracted to assess compliance with operational energy and embodied carbon requirements. These submissions were analysed at the individual‑plot level, enabling comparison of design parameters such as space heating demand, total energy use, U‑values and air permeability.

To complement this, a structured questionnaire was distributed to planning agents and consultants to gather insights into applicant experience, perceived challenges and evolving practice.
description: Data was anonymised with any personal identifying information redacted.
description: Further relevant documentation may be found in the following resources.

https://researchportal.bath.ac.uk/files/380203213/BANES_report_final.pdf
DOI: 10.5281/zenodo.18741798
title: LINF_330038200

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.auvxar
title: Occurrence Download

description: A dataset containing 78582 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ursus arctos"
 ]
}

 The dataset includes 78582 records from 350 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003352-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18741797
title: LINF_330038200

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.14734014
title: miRBench datasets

description: Changelog

PhyloP and PhastCons conservation scores for the target gene sequence have been added to the test/train/leftout datasets as two additional columns - 'gene_phyloP' and' gene_phastCons'. 

Both of new columns contain list of conservation scores rounded to 3 decimal places, one score for each nucelotide in the gene sequence.PhyloP and PhastCons scores were obtained from:



https://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw

https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phastCons100way/hg38.phastCons100way.bw


Downloaded on 15 September 2024. 

Dataset Summary

The following listed datasets were recreated via a series of post-processing pipelines (available here) to eliminate a bias between the positive and negative classes (miRNA family imbalance) discovered in previous versions of the datasets. All have a 1:1 positive to negative class ratio. 



AGO2_eCLIP_Manakov2022_leftout.tsv.gz

AGO2_eCLIP_Manakov2022_test.tsv.gz

AGO2_eCLIP_Manakov2022_train.tsv.gz

AGO2_eCLIP_Klimentova2022_test.tsv.gz

AGO2_CLASH_Hejret2023_test.tsv.gz

AGO2_CLASH_Hejret2023_train.tsv.gz


The following listed dataset is the concatenated HybriDetector output of all the selected samples from the available Manakov sample files. It therefore contains only a raw version of the positive class of the Manakov dataset. It is the input to the series of post-process pipelines for the Manakov dataset. 



AGO2_eCLIP_Manakov2022_full_dataset.tsv.gz


The other inputs to the post-process pipelines for the Hejret and Klimentova datasets are found at the following links. 



Hejret dataset

Klimentova dataset


The structure of each dataset is consistent, with the following column order:



gene: A string of length 50 indicating the binding site sequence in the 5’ to 3’ direction.

noncodingRNA: A string of variable length (16–28) indicating the mature miRNA sequence in the 5’ to 3’ direction.

noncodingRNA_name: A string indicating the name of the miRNA.

noncodingRNA_fam: A string indicating the name of the miRNA family the miRNA belongs to.

feature: A string indicating the feature annotation on the genome where the binding site occurs.

label: A boolean value indicating whether the example belongs to the positive or negative class.

chr: A string indicating the chromosome number on the genome where the binding site occurs.

start: An integer indicating the 1-based start position of the binding site on the genome.

end: An integer indicating the 1-based end position of the binding site on the genome.

strand: A string indicating whether the binding site occurs on the ’+’ or ’-’ strand on the genome.

gene_cluster_ID: An integer indicating the cluster ID of the binding site sequence used to generate the negative class.


Note that the binding sites reported in all datasets are consistent with GRCh38.
DOI: 10.5281/zenodo.11657637
title: miRBench datasets

description: Changelog

PhyloP and PhastCons conservation scores for the target gene sequence have been added to the test/train/leftout datasets as two additional columns - 'gene_phyloP' and' gene_phastCons'. 

Both of new columns contain list of conservation scores rounded to 3 decimal places, one score for each nucelotide in the gene sequence.PhyloP and PhastCons scores were obtained from:



https://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw

https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phastCons100way/hg38.phastCons100way.bw


Downloaded on 15 September 2024. 

Dataset Summary

The following listed datasets were recreated via a series of post-processing pipelines (available here) to eliminate a bias between the positive and negative classes (miRNA family imbalance) discovered in previous versions of the datasets. All have a 1:1 positive to negative class ratio. 



AGO2_eCLIP_Manakov2022_leftout.tsv.gz

AGO2_eCLIP_Manakov2022_test.tsv.gz

AGO2_eCLIP_Manakov2022_train.tsv.gz

AGO2_eCLIP_Klimentova2022_test.tsv.gz

AGO2_CLASH_Hejret2023_test.tsv.gz

AGO2_CLASH_Hejret2023_train.tsv.gz


The following listed dataset is the concatenated HybriDetector output of all the selected samples from the available Manakov sample files. It therefore contains only a raw version of the positive class of the Manakov dataset. It is the input to the series of post-process pipelines for the Manakov dataset. 



AGO2_eCLIP_Manakov2022_full_dataset.tsv.gz


The other inputs to the post-process pipelines for the Hejret and Klimentova datasets are found at the following links. 



Hejret dataset

Klimentova dataset


The structure of each dataset is consistent, with the following column order:



gene: A string of length 50 indicating the binding site sequence in the 5’ to 3’ direction.

noncodingRNA: A string of variable length (16–28) indicating the mature miRNA sequence in the 5’ to 3’ direction.

noncodingRNA_name: A string indicating the name of the miRNA.

noncodingRNA_fam: A string indicating the name of the miRNA family the miRNA belongs to.

feature: A string indicating the feature annotation on the genome where the binding site occurs.

label: A boolean value indicating whether the example belongs to the positive or negative class.

chr: A string indicating the chromosome number on the genome where the binding site occurs.

start: An integer indicating the 1-based start position of the binding site on the genome.

end: An integer indicating the 1-based end position of the binding site on the genome.

strand: A string indicating whether the binding site occurs on the ’+’ or ’-’ strand on the genome.

gene_cluster_ID: An integer indicating the cluster ID of the binding site sequence used to generate the negative class.


Note that the binding sites reported in all datasets are consistent with GRCh38.
DOI: 10.15468/dl.a6neg8
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Dutch Vegetation Database",
 "Geometry POLYGON((4.96601 52.31065,4.99427 52.31065,4.99427 52.3196,4.96601 52.3196,4.96601 52.31065))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003408-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.969dbn
title: Occurrence Download

description: A dataset containing 13327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Agapetus ochripes"
 ]
}

 The dataset includes 13327 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003409-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xyrt4n
title: Occurrence Download

description: A dataset containing 253 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Catagapetus nigrans"
 ]
}

 The dataset includes 253 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003410-260221153910048/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.cc2d2nv0
title: CCDC 2207102: Experimental Crystal Structure Determination

description: Related Article: Hui-Zi Li,  Chang-Yin Yang,  Cheng Gu,  Fei Wang,  Jian Zhang|2026|Nat.Commun.|||doi:10.1038/s41467-026-69115-7
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: 10.5517/ccdc.csd.cc2k1chh
title: CCDC 2354806: Experimental Crystal Structure Determination

description: Related Article: Hui-Zi Li,  Chang-Yin Yang,  Cheng Gu,  Fei Wang,  Jian Zhang|2026|Nat.Commun.|||doi:10.1038/s41467-026-69115-7
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: 10.5517/ccdc.csd.cc2ktgjd
title: CCDC 2377964: Experimental Crystal Structure Determination

description: Related Article: Shuai-Liang Yang, Liang Qiao, Bingyu Liu, Rui Yao, Xiao Wang, Wei Gong, Yan Liu, Jinqiao Dong, Anthony P. Davis, Yong Cui
|2026|Nat. Synth.|||doi:10.1038/s44160-025-00954-w
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: 10.5517/ccdc.csd.cc2ktglg
title: CCDC 2377966: Experimental Crystal Structure Determination

description: Related Article: Shuai-Liang Yang, Liang Qiao, Bingyu Liu, Rui Yao, Xiao Wang, Wei Gong, Yan Liu, Jinqiao Dong, Anthony P. Davis, Yong Cui
|2026|Nat. Synth.|||doi:10.1038/s44160-025-00954-w
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.vdvzme
title: Occurrence Download

description: A dataset containing 16358723 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Coleoptera)",
 "TaxonomicStatus is one of (Accepted, Synonym)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year is greater than 1980",
 "CoordinateUncertaintyInMeters is less than or equal to 18520"
 ]
}

 The dataset includes 16358723 records from 3819 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003359-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.