cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1235383
title: <i>Crassisporium</i> and <i>Romagnesiella</i>: two new genera of dark-spored Agaricales

description: A systematic study of a rare and enigmatic European species, <i>Galerina clavus</i> Romagn., is presented. Phylogenetic analyses show it to be most closely related to <i>Pachylepyrium carbonicola</i> (A.H. Sm.) Singer and <i>P. funariophilum</i> (M.M. Moser) Singer (Strophariaceae). Investigation of additional species of <i>Pachylepyrium</i> suggests this genus is polyphyletic as the type species, <i>P. fulvidula</i> (Singer) Singer, is nested in the Tubariaceae Vizzini based on multigene phylogenetic analyses. <i>Pachylepyrium nubicola</i> Singer is allied with <i>Pholiota</i> (Fr.) P. Kumm. based on high ITS similarity, and <i>P. carbonicola</i> and <i>P. funariophilum</i>, together with <i>G. clavus</i>, form a clade among a consortium of Strophariaceae Singer & A.H. Sm. and Hymenogastraceae Vittad. As a result, we propose <i>Romagnesiella</i> gen. nov. to accommodate <i>G. clavus</i>, for which a taxonomic description is given and lectotype and epitype are designated. The genus <i>Crassisporium</i> gen. nov. is proposed to encompass <i>Pachylepyrium funariophilum</i> (of which <i>P. carbonicola</i> is considered a younger taxonomic synonym), <i>P. chilense</i> M.M. Moser, and <i>P. squarrulosum</i> Singer. <i>Crassisporium</i> is distinguished from <i>Romagnesiella</i> by its thick-walled basidiospores and occurrence in burnt habitats. The identities of the morphologically similar <i>Tubaria umbonata</i> S. Lundell, <i>T. embolus</i> (Fr.) Sacc. and <i>T. minima</i> J.E. Lange are also discussed.
DOI: 10.6084/m9.figshare.1235440
title: Compounds annotated with antineoplastic agent by ChEBI

description: Supplementary data file S2 from the manuscript, 'The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research' to be published in PLOS ONE
DOI: 10.6084/m9.figshare.1235441.v1
title: % activity or IC50 values for the DRD2 receptor

description: Supplementary data file S1 from the manuscript, "The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research" to be published in PLOS ONE
DOI: 10.6084/m9.figshare.1235385.v1
title: Gaussian Job Archive for C5H13NO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1235440.v1
title: Compounds annotated with antineoplastic agent by ChEBI

description: Supplementary data file S2 from the manuscript, 'The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research' to be published in PLOS ONE
DOI: 10.6084/m9.figshare.1235383.v2
title: <i>Crassisporium</i> and <i>Romagnesiella</i>: two new genera of dark-spored Agaricales

description: A systematic study of a rare and enigmatic European species, <i>Galerina clavus</i> Romagn., is presented. Phylogenetic analyses show it to be most closely related to <i>Pachylepyrium carbonicola</i> (A.H. Sm.) Singer and <i>P. funariophilum</i> (M.M. Moser) Singer (Strophariaceae). Investigation of additional species of <i>Pachylepyrium</i> suggests this genus is polyphyletic as the type species, <i>P. fulvidula</i> (Singer) Singer, is nested in the Tubariaceae Vizzini based on multigene phylogenetic analyses. <i>Pachylepyrium nubicola</i> Singer is allied with <i>Pholiota</i> (Fr.) P. Kumm. based on high ITS similarity, and <i>P. carbonicola</i> and <i>P. funariophilum</i>, together with <i>G. clavus</i>, form a clade among a consortium of Strophariaceae Singer & A.H. Sm. and Hymenogastraceae Vittad. As a result, we propose <i>Romagnesiella</i> gen. nov. to accommodate <i>G. clavus</i>, for which a taxonomic description is given and lectotype and epitype are designated. The genus <i>Crassisporium</i> gen. nov. is proposed to encompass <i>Pachylepyrium funariophilum</i> (of which <i>P. carbonicola</i> is considered a younger taxonomic synonym), <i>P. chilense</i> M.M. Moser, and <i>P. squarrulosum</i> Singer. <i>Crassisporium</i> is distinguished from <i>Romagnesiella</i> by its thick-walled basidiospores and occurrence in burnt habitats. The identities of the morphologically similar <i>Tubaria umbonata</i> S. Lundell, <i>T. embolus</i> (Fr.) Sacc. and <i>T. minima</i> J.E. Lange are also discussed.
DOI: 10.6084/m9.figshare.1235300.v1
title: A computed mechanistic pathway for the formation of an amide from an acid and an amine in non-polar solution.

description: The mechanistic pathway for the formation of an amide from a primary amine and a carboxylic acid, evaluated using potential energy surfaces computed at the wB97XD/6-311G(d,p) and the B2PLYP+D3/TZVP procedures, with a an applied continuum solvent field for p-xylene.
DOI: 10.6084/m9.figshare.1235383.v1
title: <i>Crassisporium</i> and <i>Romagnesiella</i>: two new genera of dark-spored Agaricales

description: A systematic study of a rare and enigmatic European species, <i>Galerina clavus</i> Romagn., is presented. Phylogenetic analyses show it to be most closely related to <i>Pachylepyrium carbonicola</i> (A.H. Sm.) Singer and <i>P. funariophilum</i> (M.M. Moser) Singer (Strophariaceae). Investigation of additional species of <i>Pachylepyrium</i> suggests this genus is polyphyletic as the type species, <i>P. fulvidula</i> (Singer) Singer, is nested in the Tubariaceae Vizzini based on multigene phylogenetic analyses. <i>Pachylepyrium nubicola</i> Singer is allied with <i>Pholiota</i> (Fr.) P. Kumm. based on high ITS similarity, and <i>P. carbonicola</i> and <i>P. funariophilum</i>, together with <i>G. clavus</i>, form a clade among a consortium of Strophariaceae Singer & A.H. Sm. and Hymenogastraceae Vittad. As a result, we propose <i>Romagnesiella</i> gen. nov. to accommodate <i>G. clavus</i>, for which a taxonomic description is given and lectotype and epitype are designated. The genus <i>Crassisporium</i> gen. nov. is proposed to encompass <i>Pachylepyrium funariophilum</i> (of which <i>P. carbonicola</i> is considered a younger taxonomic synonym), <i>P. chilense</i> M.M. Moser, and <i>P. squarrulosum</i> Singer. <i>Crassisporium</i> is distinguished from <i>Romagnesiella</i> by its thick-walled basidiospores and occurrence in burnt habitats. The identities of the morphologically similar <i>Tubaria umbonata</i> S. Lundell, <i>T. embolus</i> (Fr.) Sacc. and <i>T. minima</i> J.E. Lange are also discussed.
DOI: 10.6084/m9.figshare.1235151
title: Gaussian Job Archive for C5H13NO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1235151.v1
title: Gaussian Job Archive for C5H13NO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1235149
title: Gaussian Job Archive for C5H13NO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1234130
title: FileRemoved

description: File removed for redundancy
DOI: 10.6084/m9.figshare.1234129
title: Environmental Dashboard Dataset 2013

description: File removed for redundancy<br>
DOI: 10.6084/m9.figshare.1234130.v1
title: Environmental Dashboard Dataset 2012

description: Dataset looking at systems thinking as a result of passive exposure to an "environmental dashboard"
DOI: 10.6084/m9.figshare.1235149.v1
title: Gaussian Job Archive for C5H13NO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1234127
title: Poster Trastornos de Ansiedad

description: Poster Trastornos de Ansiedad
DOI: 10.6084/m9.figshare.1234128
title: Environmental Dashboard Text File

description: Text file explaining the variables in the files 'Environmental Dashboard Dataset 2012' and 'Environmental Dashboard Dataset 2013'
DOI: 10.6084/m9.figshare.1234103
title: Attitudes in Ireland to Unmarried Mothers and their Children (1900s-1970s)

description: Overview
DOI: 10.6084/m9.figshare.1234128.v1
title: Environmental Dashboard Text File

description: Text file explaining the variables in the files 'Environmental Dashboard Dataset 2012' and 'Environmental Dashboard Dataset 2013'
DOI: 10.6084/m9.figshare.1234089
title: Two social network datasets for the accepted manuscript titled "Relational diversity promotes cooperation in prisoner's dilemma games" in Plos One

description: These are the two social network datasets for the accepted manuscript titled "Relational diversity promotes cooperation in prisoner's dilemma games" in Plos One. All datasets are collected from Facebook.com.
DOI: 10.6084/m9.figshare.1234103.v1
title: Attitudes in Ireland to Unmarried Mothers and their Children (1900s-1970s)

description: Overview
DOI: 10.6084/m9.figshare.1234088
title: Compare the abundance of insects in grassland at day and night

description: Experiment is to colleting the abundance of insects in grassland at day and night respectively. Experiment is took place in grassland where near the Stong Pond, York University and conducted for one week . 15 pitfall traps were set every 5 meters, and the data was collected twice one day at 8:00am and 8:00pm respectively.
DOI: 10.15468/dl.qatvxu
title: Occurrence Download

description: A dataset containing 1066 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Synageles venator (Lucas, 1836)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 1066 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095365-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10277187
title: spotless-benchmark-datasets

description: In standards.tar.gz, the silver standards are formatted as silver_standard_i-j, where i refers to the originating single-cell dataset and j refers to the synthspot abundance pattern. Each directory of the silver standard contains 10 replicates. All reference datasets are in the 'reference/' folder.
Single-cell dataset:

Brain cortex
Single-cell cerebellum
Single-nucleus cerebellum
Hippocampus
Kidney
Squamous cell carcinoma
Melanoma
Abundance patterns:

Uniform distinct
Diverse distinct
Uniform overlap
Diverse overlap
Dominant cell type
Partially dominant cell type
Rare cell type
Regionally rare cell type
Missing cell types
To use liver_dataset.tar.gz, please read liver_README.txt before proceeding.
We only uploaded .rds files to keep the file size smaller. For more information on file conversion, please visit the GitHub repository.
DOI: 10.5281/zenodo.5727614
title: spade-benchmark-datasets

description: The bronze standards are formatted as bronze_standard_<strong>i</strong>-<strong>j</strong>, where <strong>i </strong>refers to the originating single-cell dataset and j refers to the synthvisium dataset type. Each directory of the bronze standard contains 10 replicates. <strong>i</strong> <strong>single-cell dataset</strong> <strong>j</strong> <strong>synthvisium dataset type</strong> 1 brain cortex 1 artificial_uniform_distinct 2 single-cell cerebellum 2 artificial_diverse_distinct 3 single-nucleus cerebellum 3 artificial_uniform_overlap 4 hippocampus 4 artificial_diverse_overlap 5 kidney 5 artificial_dominant_celltype_diverse 6 pbmc 6 artificial_partially_dominant_celltype_diverse 7 scc_p5 7 artificial_dominant_rare_celltype_diverse 8 artificial_regional_rare_celltype_diverse
DOI: 10.5281/zenodo.11074215
title: Benchmark datasets for Spotless

description: In standards.tar.gz, the silver standards are formatted as silver_standard_i-j, where i refers to the originating single-cell dataset and j refers to the synthspot abundance pattern. Each directory of the silver standard contains 10 replicates. All reference datasets are in the 'reference/' folder.

Single-cell dataset:



Brain cortex

Single-cell cerebellum

Single-nucleus cerebellum

Hippocampus

Kidney

Squamous cell carcinoma

Melanoma


Abundance patterns:



Uniform distinct

Diverse distinct

Uniform overlap

Diverse overlap

Dominant cell type

Partially dominant cell type

Rare cell type

Regionally rare cell type

Missing cell types


To use liver_dataset.tar.gz, please read liver_README.txt before proceeding.

dataset_visualizations.zip contain visualizations of the gold standard, silver standard, and case study datasets.

We only uploaded .rds files to keep the file size smaller. For more information on file conversion, please visit the GitHub repository.
DOI: 10.5281/zenodo.13373946
title: Benchmark datasets for Spotless

description: In standards.tar.gz, the silver standards are formatted as silver_standard_i-j, where i refers to the originating single-cell dataset and j refers to the synthspot abundance pattern. Each directory of the silver standard contains 10 replicates. All reference datasets are in the 'reference/' folder.

Single-cell dataset:



Brain cortex

Single-cell cerebellum

Single-nucleus cerebellum

Hippocampus

Kidney

Squamous cell carcinoma

Melanoma


Abundance patterns:



Uniform distinct

Diverse distinct

Uniform overlap

Diverse overlap

Dominant cell type

Partially dominant cell type

Rare cell type

Regionally rare cell type

Missing cell types


We only uploaded .rds files to keep the file size smaller. For more information on file conversion, please visit the GitHub repository.

To use liver_dataset.tar.gz, please read liver_README.txt before proceeding.

dataset_visualizations.zip contain visualizations of the gold standard, silver standard, and case study datasets.

raw_results.zip contains the proportions and evaluation metrics of each method, as well as aggregated metrics used to generate plots. They can be used in tandem with the scripts in the GitHub repository.
DOI: 10.5281/zenodo.5763377
title: spade-benchmark-datasets

description: The bronze standards are formatted as bronze_standard_<strong>i</strong>-<strong>j</strong>, where <strong>i </strong>refers to the originating single-cell dataset and j refers to the synthvisium dataset type. Each directory of the bronze standard contains 10 replicates. <strong>i</strong> <strong>single-cell dataset</strong> <strong>j</strong> <strong>synthvisium dataset type</strong> 1 brain cortex 1 artificial_uniform_distinct 2 single-cell cerebellum 2 artificial_diverse_distinct 3 single-nucleus cerebellum 3 artificial_uniform_overlap 4 hippocampus 4 artificial_diverse_overlap 5 kidney 5 artificial_dominant_celltype_diverse 6 pbmc 6 artificial_partially_dominant_celltype_diverse 7 scc_p5 7 artificial_dominant_rare_celltype_diverse 8 artificial_regional_rare_celltype_diverse
DOI: 10.5281/zenodo.6786528
title: spotless-benchmark-datasets

description: The silver standards are formatted as silver_standard_<strong>i</strong>-<strong>j</strong>, where <strong>i </strong>refers to the originating single-cell dataset and j refers to the synthvisium dataset type. Each directory of the silver standard contains 10 replicates. <strong>i</strong> <strong>single-cell dataset</strong> <strong>j</strong> <strong>synthvisium dataset type</strong> 1 brain cortex 1 artificial_uniform_distinct 2 single-cell cerebellum 2 artificial_diverse_distinct 3 single-nucleus cerebellum 3 artificial_uniform_overlap 4 hippocampus 4 artificial_diverse_overlap 5 kidney 5 artificial_dominant_celltype_diverse 6 pbmc 6 artificial_partially_dominant_celltype_diverse 7 scc_p5 7 artificial_dominant_rare_celltype_diverse 8 artificial_regional_rare_celltype_diverse
DOI: 10.5281/zenodo.8211492
title: spotless-benchmark-datasets

description: In <strong>standards.tar.gz</strong>, the silver standards are formatted as silver_standard_<strong>i</strong>-<strong>j</strong>, where <strong>i </strong>refers to the originating single-cell dataset and j refers to the <em>synthspot</em> abundance pattern. Each directory of the silver standard contains 10 replicates. <strong>i</strong> <strong>single-cell dataset</strong> <strong>j</strong> <strong>synthvisium dataset type</strong> 1 brain cortex 1 artificial_uniform_distinct 2 single-cell cerebellum 2 artificial_diverse_distinct 3 single-nucleus cerebellum 3 artificial_uniform_overlap 4 hippocampus 4 artificial_diverse_overlap 5 kidney 5 artificial_dominant_celltype_diverse 6 scc_p5 6 artificial_partially_dominant_celltype_diverse 7 artificial_dominant_rare_celltype_diverse 8 artificial_regional_rare_celltype_diverse 9 artificial_missing_celltypes_visium All reference datasets are in the 'reference/' folder. To use <strong>liver_dataset.tar.gz, </strong>please read liver_README.txt before proceeding.
DOI: 10.5281/zenodo.5727613
title: Benchmark datasets for Spotless

description: In standards.tar.gz, the silver standards are formatted as silver_standard_i-j, where i refers to the originating single-cell dataset and j refers to the synthspot abundance pattern. Each directory of the silver standard contains 10 replicates. All reference datasets are in the 'reference/' folder.

Single-cell dataset:



Brain cortex

Single-cell cerebellum

Single-nucleus cerebellum

Hippocampus

Kidney

Squamous cell carcinoma

Melanoma


Abundance patterns:



Uniform distinct

Diverse distinct

Uniform overlap

Diverse overlap

Dominant cell type

Partially dominant cell type

Rare cell type

Regionally rare cell type

Missing cell types


We only uploaded .rds files to keep the file size smaller. For more information on file conversion, please visit the GitHub repository.

To use liver_dataset.tar.gz, please read liver_README.txt before proceeding.

dataset_visualizations.zip contain visualizations of the gold standard, silver standard, and case study datasets.

raw_results.zip contains the proportions and evaluation metrics of each method, as well as aggregated metrics used to generate plots. They can be used in tandem with the scripts in the GitHub repository.
DOI: 10.5281/zenodo.7781323
title: spotless-benchmark-datasets

description: The silver standards are formatted as silver_standard_<strong>i</strong>-<strong>j</strong>, where <strong>i </strong>refers to the originating single-cell dataset and j refers to the <em>synthspot</em> abundance pattern. Each directory of the silver standard contains 10 replicates. <strong>i</strong> <strong>single-cell dataset</strong> <strong>j</strong> <strong>synthvisium dataset type</strong> 1 brain cortex 1 artificial_uniform_distinct 2 single-cell cerebellum 2 artificial_diverse_distinct 3 single-nucleus cerebellum 3 artificial_uniform_overlap 4 hippocampus 4 artificial_diverse_overlap 5 kidney 5 artificial_dominant_celltype_diverse 6 scc_p5 6 artificial_partially_dominant_celltype_diverse 7 artificial_dominant_rare_celltype_diverse 8 artificial_regional_rare_celltype_diverse 9 artificial_missing_celltypes_visium All reference datasets are in the 'reference/' folder.
DOI: 10.15468/dl.6jns4m
title: Occurrence Download

description: A dataset containing 237 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Saldula pilosella (Thomson, 1871)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 237 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095366-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k9hy62
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Carabus heteromorphus K.Daniel, 1896",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095368-240626123714530/datasets/export for details.
DOI: 10.15468/dl.h6ra2u
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Centaurea leptophylla (K.Koch) Tchich.)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095370-240626123714530/datasets/export for details.
DOI: 10.15468/dl.t7q393
title: Occurrence Download

description: A dataset containing 10585 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Alopecosa pulverulenta (Clerck, 1757)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 10585 records from 246 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095369-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7su288
title: Occurrence Download

description: A dataset containing 60794 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Martes martes (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 60794 records from 876 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095367-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4121/922d30de-a26b-4c81-8644-ad036182239c.v1
title: Data and code underlying the publication: Multi-decadal fluctuations in root zone storage capacity through vegetation adaptation to hydro-climatic variability has minor effects on the hydrological response in the Neckar basin, Germany

description: The semi-distributed hydrological model codes, which can be used to estimate the root zone storage capacity based on calibration. The model codes are also used to quantity the effects of time-variant root zone storage capacity on hydrological response.
DOI: 10.15468/dl.fk4czj
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Synageles pulcher Franganillo, 1913",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095371-240626123714530/datasets/export for details.