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

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Askidiosperma insigne (Pillans) H.Linder",
 "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 -23.2724,25.1306 -24.0715,25.5395 -24.0715,25.5395 -23.2724))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044583-250525065834625/datasets/export for details.
DOI: 10.15468/dl.t5c2gh
title: Occurrence Download

description: A dataset containing 4588 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gladiolus illyricus W.D.J.Koch",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4588 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044582-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fp7bq5
title: Occurrence Download

description: A dataset listing the 1065 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-80.50553 37.13903, -80.18368 37.25616, -80.40822 37.52714, -80.72444 37.4178, -80.50553 37.13903))",
 "TaxonKey is Plantae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material sample, Material citation)"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED, CULTIVATED)"
 ]
 }
 }
 ]
}

 The dataset's 1065 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044569-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15660395
title: netta_peposaca_spades_01.fasta.gz
DOI: 10.5281/zenodo.15660396
title: netta_peposaca_spades_01.fasta.gz
DOI: 10.15468/dl.abxvme
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gomphonema clavatum Agardh",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044586-250525065834625/datasets/export for details.
DOI: 10.15468/dl.6kudqv
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Askidiosperma insigne (Pillans) H.Linder",
 "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 ((20.2855 -34.7533,20.509 -34.5676,20.509 -32.9007,17.7723 -32.9007,17.8156 -33.0786,18.3471 -33.7176,18.3748 -33.8287,18.2181 -34.0492,18.3197 -34.3408,18.4452 -34.429,18.5435 -34.4213,18.5872 -34.3667,18.5363 -34.167,18.7345 -34.1508,18.7216 -34.3637,18.7808 -34.4521,19.0289 -34.4206,19.0831 -34.4835,19.2655 -34.5017,19.2032 -34.6157,19.2394 -34.6926,19.375 -34.6963,19.6091 -34.8524,19.8251 -34.8396,19.9798 -34.9064,20.1081 -34.8731,20.1517 -34.7847,20.2855 -34.7533))"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044585-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15660501
title: Tonsil Atlas: CellRanger outputs

description: This repository contains all the expression and accessibility matrices for each of the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) associated with the article "An Atlas of Cells in The Human Tonsil," published in Immunity in 2024. In particular, each modality was produced with different platforms from 10X Genomics and processed with different versions of CellRanger. This repository contains the most important outputs from each CellRanger run of each library. In addition, it also includes de expression and accessiblity matrices for the two mantle cell lymphoma (MCL) patients analyzed in the paper.

Version 4.0 of this repository adds all high-quality TIFF images of the Visium slides, as requested by a user.
description: Structure

For each modality, the first folders represent a "subproject", which you can view as one run of the 10X Chromium. Inside it, you will find all the gel-bead-in-emulsion ids (GEM ids), which correspond to the output from a single 10X Chip Channel (see Cellranger glossary for more information). Inside each GEM-specific folder, you can find the most relevant files from the "outs" folder produced by CR. This include the expression/accessibility matrices, fragment files, web summaries (html with QC reports), and more. Here you can find a more detailed explanation of every output.To access processed data in the form of Seurat objects please check this other Zenodo repository. To access the data, documentation and reasoning behind each annotation in the tonsil atlas, please check the HCATonsilData package. Finally, to annotate cells from secondary lymphoid organs using the tonsil atlas as reference, check the Azimuth reference.

Metadata

We provide two levels of metadata:- Donor-level metadata: file "tonsil_atlas_donor_metadata.csv". For each of the 17 donors, this file specifies the hospital in which the tonsil was sampled (Clinic, CIMA or Newcastle), the sex, age, age group (child, young adult or old adult), the reason for tonsillectomy (tonsillitis, sleep apnea, or surgery for another condition), and the cohort type (discovery or validation). Note that for the four tonsils sampled in Newcastle we include the link between the original ids and the ones specific for this article (e.g. BCLL-20-T / TIP01)- Library-specific metadata: for each sequencing library, this metadata documents the subproject, GEM well (10X Chip Channel, see above), library name, library id, library type, and donor id. The donor_id column allows to link this table with the previous one (donor-level), and the gem_id column is important to understand which libraries were derived from the same GEM well. For instance, multiome GEM wells contain two library_ids per GEM well (RNA+ATAC).
DOI: 10.5281/zenodo.6678330
title: Tonsil Atlas: CellRanger outputs

description: This repository contains all the expression and accessibility matrices for each of the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) associated with the article "An Atlas of Cells in The Human Tonsil," published in Immunity in 2024. In particular, each modality was produced with different platforms from 10X Genomics and processed with different versions of CellRanger. This repository contains the most important outputs from each CellRanger run of each library. In addition, it also includes de expression and accessiblity matrices for the two mantle cell lymphoma (MCL) patients analyzed in the paper.

Version 4.0 of this repository adds all high-quality TIFF images of the Visium slides, as requested by a user.
description: Structure

For each modality, the first folders represent a "subproject", which you can view as one run of the 10X Chromium. Inside it, you will find all the gel-bead-in-emulsion ids (GEM ids), which correspond to the output from a single 10X Chip Channel (see Cellranger glossary for more information). Inside each GEM-specific folder, you can find the most relevant files from the "outs" folder produced by CR. This include the expression/accessibility matrices, fragment files, web summaries (html with QC reports), and more. Here you can find a more detailed explanation of every output.To access processed data in the form of Seurat objects please check this other Zenodo repository. To access the data, documentation and reasoning behind each annotation in the tonsil atlas, please check the HCATonsilData package. Finally, to annotate cells from secondary lymphoid organs using the tonsil atlas as reference, check the Azimuth reference.

Metadata

We provide two levels of metadata:- Donor-level metadata: file "tonsil_atlas_donor_metadata.csv". For each of the 17 donors, this file specifies the hospital in which the tonsil was sampled (Clinic, CIMA or Newcastle), the sex, age, age group (child, young adult or old adult), the reason for tonsillectomy (tonsillitis, sleep apnea, or surgery for another condition), and the cohort type (discovery or validation). Note that for the four tonsils sampled in Newcastle we include the link between the original ids and the ones specific for this article (e.g. BCLL-20-T / TIP01)- Library-specific metadata: for each sequencing library, this metadata documents the subproject, GEM well (10X Chip Channel, see above), library name, library id, library type, and donor id. The donor_id column allows to link this table with the previous one (donor-level), and the gem_id column is important to understand which libraries were derived from the same GEM well. For instance, multiome GEM wells contain two library_ids per GEM well (RNA+ATAC).
DOI: 10.15468/dl.kv6a65
title: Occurrence Download

description: A dataset listing the 1065 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-80.50553 37.13903, -80.18368 37.25616, -80.40822 37.52714, -80.72444 37.4178, -80.50553 37.13903))",
 "TaxonKey is Plantae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material sample, Material citation)"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED, CULTIVATED)"
 ]
 }
 }
 ]
}

 The dataset's 1065 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044572-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tkgsr3
title: Occurrence Download

description: A dataset containing 208011 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Haemorhous mexicanus (P.L.Statius Müller, 1776)"
 ]
}

 The dataset includes 208011 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044564-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zp2273
title: Occurrence Download

description: A dataset containing 23388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Globularia alypum L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 23388 records from 200 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044587-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jnhgva
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Pristidactylus fasciatus (D'Orbigny & Bibron, 1837), Leiosaurus jaguaris Laspiur, Acosta & Abdala, 2007)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044589-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wysq5c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gomphonema clavatum Agardh",
 "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 ((27.1332 -20.158,25.5395 -23.2724,25.5395 -24.0715,30.5701 -24.0715,30.5701 -20.3186,29.6496 -19.6123,28.947 -19.4003,28.1821 -19.4609,27.6072 -19.7214,27.1332 -20.158))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044588-250525065834625/datasets/export for details.
DOI: 10.15468/dl.pxnb7j
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Askidiosperma insigne (Pillans) H.Linder",
 "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 ((35.628 -23.023,35.6007 -22.9702,35.6007 -23.165,35.628 -23.023))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044590-250525065834625/datasets/export for details.
DOI: 10.15468/dl.e9z2af
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gomphonema clavatum Agardh",
 "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 ((25.0214 -34.0501,25.5395 -34.1098,25.5395 -32.9007,20.509 -32.9007,20.509 -34.5676,20.524 -34.555,20.8859 -34.5419,20.9606 -34.4398,21.2995 -34.5131,21.5296 -34.4338,21.8696 -34.4439,22.0323 -34.2835,22.221 -34.2428,22.2566 -34.1304,22.5993 -34.0741,22.9652 -34.1674,23.4069 -34.1858,23.4955 -34.0792,23.6056 -34.0563,24.8471 -34.2877,24.9447 -34.2397,25.0214 -34.0501))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044591-250525065834625/datasets/export for details.
DOI: 10.15468/dl.khkfvv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Askidiosperma insigne (Pillans) H.Linder",
 "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 ((35.6306 -23.844,35.6007 -23.8125,35.6007 -24.0157,35.6306 -23.844))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044593-250525065834625/datasets/export for details.
DOI: 10.15468/dl.jqg3gw
title: Occurrence Download

description: A dataset containing 12491 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Globularia vulgaris L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12491 records from 212 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044595-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5dsc3r
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atriplex polycarpa (Torr.) S.Watson)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Absent",
 "Country is United States of America",
 "StateProvince is California"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044600-250525065834625/datasets/export for details.
DOI: 10.15468/dl.vw26ea
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gomphonema clavatum Agardh",
 "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 ((32.064 -28.9416,32.4847 -28.5786,30.5701 -28.5786,30.5701 -30.7329,30.6252 -30.6659,31.4179 -29.4257,31.8178 -29.0299,32.064 -28.9416))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044596-250525065834625/datasets/export for details.
DOI: 10.15468/dl.nbfnbb
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chenolea diffusa Thunb.",
 "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 ((30.0251 -31.3959,30.5701 -30.7329,30.5701 -28.5786,25.5395 -28.5786,25.5395 -32.9007,28.2048 -32.9007,28.5753 -32.6569,29.4902 -31.7517,30.0251 -31.3959))"
 ]
}

 The dataset includes 19 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044599-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4dzqah
title: Occurrence Download

description: A dataset containing 346 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vespa soror Buysson, 1905)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 346 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044597-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nxx97s
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is Pristidactylus volcanensis Lamborot & Diaz, 1987"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044598-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e2h294
title: Occurrence Download

description: A dataset containing 21879 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "TaxonKey is Phaeophyceae"
 ]
}

 The dataset includes 21879 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044601-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.42jx5m
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gomphonema clavatum Agardh",
 "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 ((35.5808 -24.13,35.5909 -24.0715,30.5701 -24.0715,30.5701 -28.5786,32.4847 -28.5786,32.55 -28.5222,33.0346 -26.8668,32.9741 -26.7838,33.0415 -26.059,32.9304 -26.0011,32.7994 -26.1281,32.6834 -26.0015,32.813 -25.8728,32.8513 -25.7166,33.3048 -25.3731,35.1489 -24.6699,35.5808 -24.13))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044603-250525065834625/datasets/export for details.
DOI: 10.15468/dl.rb69mw
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "TaxonKey is one of (Hemidactylus palaichthus Kluge, 1969)"
 ]
}

 The dataset includes 177 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044606-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.emtud6
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chenolea diffusa Thunb.",
 "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 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044605-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d9q53j
title: Occurrence Download

description: A dataset containing 21879 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "TaxonKey is Phaeophyceae"
 ]
}

 The dataset includes 21879 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044602-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4346v
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "TaxonKey is Pristidactylus araucanus (Gallardo, 1964)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044607-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.