cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4g3woi
title: Occurrence Download

description: A dataset containing 276189 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "PublishingCountry is China"
 ]
}

 The dataset includes 276189 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029912-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n7agh8
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Vernonia attenuata Wall. ex DC."
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0323739-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x94crw
title: Occurrence Download

description: A dataset containing 37950 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cotoneaster integerrimus Medik.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 37950 records from 339 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002778-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.juzkex
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potentilla nivea L.",
 "MediaType is Image",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 157 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0408952-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5w84vp
title: Occurrence Download

description: A dataset containing 92035 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Campanula rapunculoides L.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 92035 records from 600 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002128-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t4nfx4
title: Occurrence Download

description: A dataset containing 437 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Alouatta caraya (Humboldt, 1812)",
 "Year 1970-2022"
 ]
}

 The dataset includes 437 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0270077-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hgch3e
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cuora trifasciata (Bell, 1825)"
 ]
}

 The dataset includes 135 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0173719-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f8bkdx
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Kenya",
 "TaxonKey is Afrocarpus usambarensis (Pilg.) C.N.Page"
 ]
}

 The dataset includes 9 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001213-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ghvgcd
title: Occurrence Download

description: A dataset containing 2555 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Prionailurus bengalensis (Kerr, 1792)",
 "TaxonKey is Panthera tigris (Linnaeus, 1758)"
 ]
}

 The dataset includes 2555 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029908-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11386932
title: Case study in Ouray (Colorado, USA)

description: The dataset is located in Ouray, Colorade, USA. It is the point clouds collected by an Optech ILRIS-3D laser scanner at four scan positions in 2004 from Lato et al., 2013. The scanning time was about 15 min, the resolution was about 2 cm, and there was a total of 1,515,722 points.
DOI: 10.5281/zenodo.11386933
title: Case study in Ouray (Colorado, USA)

description: The dataset is located in Ouray, Colorade, USA. It is the point clouds collected by an Optech ILRIS-3D laser scanner at four scan positions in 2004 from Lato et al., 2013. The scanning time was about 15 min, the resolution was about 2 cm, and there was a total of 1,515,722 points.
DOI: 10.15468/dl.kfkrz0
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glaziophyton Franch."
 ]
}

 The dataset includes 52 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029909-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tmh28c
title: Occurrence Download

description: A dataset containing 716 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Harpia harpyja (Linnaeus, 1758)",
 "Year 2000-2020"
 ]
}

 The dataset includes 716 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181885-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z744d2
title: Occurrence Download

description: A dataset containing 1967702 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Korea, Republic of",
 "PublishingOrg is 6f2da4d9-8bd9-4f4f-852b-22cde4a43a01"
 ]
}

 The dataset includes 1967702 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001212-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trbxh2
title: Occurrence Download

description: A dataset containing 729 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cercosaura argulus Peters, 1862"
 ]
}

 The dataset includes 729 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186438-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dwsqke
title: Occurrence Download

description: A dataset containing 49072 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "Geometry POLYGON((-107.95166 18.85254,-91.97754 13.79883,-84.44092 20.74219,-97.229 27.50977,-105.5127 32.16797,-118.32275 33.22266,-117.09229 29.39941,-107.95166 18.85254))",
 "HasCoordinate is true",
 "TaxonKey is Tyrannidae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 49072 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029910-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bh8qud
title: Occurrence Download

description: A dataset containing 772 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Freshwater Lamprey Survey Data",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 772 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002136-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10692018
title: Wei et al. 2024

description: Processed data for Wei et al. "High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment"

the scanpy object contains raw (cellbender) and normalized counts, two UMAPs for all cells and epithelial cells only, respectively, and the following meta-data columns:



sample: sample ID

sample_origin: tumour or normal

patient: patient ID

MS_status: MSI or MSS

n_counts: # of UMIs per cell

n_genes: # of gnes per cells

S_score: score for S phase

G2M_score: score of G2/M phase

cell_type_coarse: low-resolution cell type annotation (epithelial vs. immune vs. stromal)

cell_type_fine: high-resolution cell type annotation (by label transfer from Uhlitz et al.)

CCISM_call: cell assignment by CCISM

CCISM_score: score from CCISM

numbat_call: assignment by numbat

numbat_score: score from numbat

inferCNV_call:  assignment from inferCNV

iCMS_call: assignment using iCMS signatures

consensus_call: numbat/CCISM consensus identity

cell_type_epi: epithelial cell type (combining TC1-4 from Uhlitz et al., and labeling cells defined here as genomically cancer as Tumour)

cytotrace_pseudotime: pseudotime from cytotrace

louvain: louvain clusters for epithelial cells


list of processed data used to create this object



folder cellranger contains raw feature barcode matrices for single-cell RNAseq data of 10 patients

folder cellbender contains filtered feature barcode matrices after background removal

folder WGS contains vcf.gz results from somatic variant calling with mutect2

folder cellSNP contains `cellsnp-lite` output: counts of total and alternative alleles observed for somatic variants in scRNAseq data; subfolder downsampled contains results after downsampling bam files to 5, 10, 20 or 50% of reads

folder numbat contains final clone assignments by Numbat


in addition, the folder LUNG contains processed data for six lung adenocarcinoma cases from Bischof et al. [doi:10.1038/s41388-021-02054-3.] 



subfolder WGS contains .vcf.gz results from somatic variant calling with mutect2

subfolder cellSNP contains `cellsnp-lite` output: counts of total and alternative alleles observed for somatic variants in scRNAseq data
DOI: 10.5281/zenodo.11348062
title: Wei et al. 2024

description: Processed data for Wei et al. "High-confidence calling of normal epithelial cells allows identification of a novel stem-like cell state in the colorectal cancer microenvironment"

the scanpy object contains raw (cellbender) and normalized counts, two UMAPs for all cells and epithelial cells only, respectively, and the following meta-data columns:



sample: sample ID

sample_origin: tumour or normal

patient: patient ID

MS_status: MSI or MSS

n_counts: # of UMIs per cell

n_genes: # of gnes per cells

S_score: score for S phase

G2M_score: score of G2/M phase

cell_type_coarse: low-resolution cell type annotation (epithelial vs. immune vs. stromal)

cell_type_fine: high-resolution cell type annotation (by label transfer from Uhlitz et al.)

CCISM_call: cell assignment by CCISM

CCISM_score: score from CCISM

numbat_call: assignment by numbat

numbat_score: score from numbat

inferCNV_call:  assignment from inferCNV

iCMS_call: assignment using iCMS signatures

consensus_call: numbat/CCISM consensus identity

cell_type_epi: epithelial cell type (combining TC1-4 from Uhlitz et al., and labeling cells defined here as genomically cancer as Tumour)

cytotrace_pseudotime: pseudotime from cytotrace

louvain: louvain clusters for epithelial cells


list of processed data used to create this object



folder cellranger contains raw feature barcode matrices for single-cell RNAseq data of 10 patients

folder cellbender contains filtered feature barcode matrices after background removal

folder WGS contains vcf.gz results from somatic variant calling with mutect2

folder cellSNP contains `cellsnp-lite` output: counts of total and alternative alleles observed for somatic variants in scRNAseq data; subfolder downsampled contains results after downsampling bam files to 5, 10, 20 or 50% of reads

folder numbat contains final clone assignments by Numbat


in addition, the folder LUNG contains processed data for six lung adenocarcinoma cases from Bischof et al. [doi:10.1038/s41388-021-02054-3.] 



subfolder WGS contains .vcf.gz results from somatic variant calling with mutect2

subfolder cellSNP contains `cellsnp-lite` output: counts of total and alternative alleles observed for somatic variants in scRNAseq data
DOI: 10.15468/dl.5xjavq
title: Occurrence Download

description: A dataset containing 22361 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Leopardus jacobitus (Cornalia, 1865), Leopardus Gray, 1842)"
 ]
}

 The dataset includes 22361 records from 451 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046580-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rx627y
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aedes aegypti (Linnaeus, 1762)",
 "Country is Peru",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 106 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030677-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uetebh
title: Occurrence Download

description: A dataset containing 776 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lampropeltis alterna (Brown, 1901)"
 ]
}

 The dataset includes 776 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030678-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k94pmz
title: Occurrence Download

description: A dataset containing 361 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Macropsis infuscata (Sahlberg, 1871)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 361 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015709-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qqfhqk
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Ceratozamia rosea Perez-Farr., Gut.Ortega & Vovides, 2023"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015710-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y96swy
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-140.04558 59.69516,-132.9279 59.69516,-132.9279 62.13487,-140.04558 62.13487,-140.04558 59.69516))",
 "TaxonKey is Pherbellia albocostata (Fallén, 1820)"
 ]
}

 The dataset includes 29 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015711-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2zxqj6
title: Occurrence Download

description: A dataset containing 183394 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myotis daubentonii (Kuhl, 1817)"
 ]
}

 The dataset includes 183394 records from 2245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015700-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1116653.10fu
title: SH1116653.10FU

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/sh1116654.10fu
title: SH1116654.10FU

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/sh1116655.10fu
title: SH1116655.10FU

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/sh1116656.10fu
title: SH1116656.10FU

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/sh1116658.10fu
title: SH1116658.10FU

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/sh1116659.10fu
title: SH1116659.10FU

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.