cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.6khpjx
title: Occurrence Download

description: A dataset containing 332515 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Humulus lupulus L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 332515 records from 1627 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109955-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bgmaf8
title: Occurrence Download

description: A dataset containing 4916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1970-2000",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Urena lobata L.",
 "TaxonKey is Musa acuminata Colla",
 "TaxonKey is Hibiscus cannabinus L.",
 "TaxonKey is Boesenbergia rotunda (L.) Mansf.",
 "TaxonKey is Hodgsonia heteroclita (Roxb.) Hook.fil. & Thomson",
 "TaxonKey is Triticum urartu Thumanjan ex Gandilyan",
 "TaxonKey is Aegilops tauschii Coss.",
 "TaxonKey is Triticum boeoticum Boiss.",
 "TaxonKey is Triticum dicoccoides (Körnicke) G.Schweinfurth",
 "TaxonKey is Eleusine africana Kenn.-O'Byrne"
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4916 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013458-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eugnfd
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pitcairnia prolifera Rauh"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001917-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dzw2yc
title: Occurrence Download

description: A dataset containing 62277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "TaxonKey is Vulpes vulpes (Linnaeus, 1758)"
 ]
}

 The dataset includes 62277 records from 126 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0251354-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g2egf5
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Leucophaeus pipixcan (Wagler, 1831)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086711-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.za2drx
title: Occurrence Download

description: A dataset containing 303 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "DatasetKey is FloraCAT: Banco de datos de los cormófitos de Cataluña",
 "DatasetKey is CSIC-Real Jardín Botánico-Anthos. Sistema de Información de las Plantas de España",
 "DatasetKey is Institut Botanic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), BC-Plantae",
 "DatasetKey is Flora d'Andorra"
 ]
 },
 {
 "or" : [
 "TaxonKey is Aquilegia hirsutissima Timb.-Lagr.",
 "TaxonKey is Achillea chamaemelifolia Pourr."
 ]
 }
 ]
}

 The dataset includes 303 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013460-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jqhqjp
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gerbillus syrticus Misonne, 1974"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001917-171020152545675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7qbrg
title: Occurrence Download

description: A dataset containing 1593 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-127.79297 17.27512,-52.91016 17.27512,-52.91016 51.37726,-127.79297 51.37726,-127.79297 17.27512))",
 "HasGeospatialIssue is false",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 1593 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0272792-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qksol6
title: Occurrence Download

description: A dataset containing 1326 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "DecimalLatitude is greater than 13.0976356322029",
 "DecimalLatitude is less than 13.7525328976473",
 "DecimalLongitude is greater than 144.368091094277",
 "DecimalLongitude is less than 145.01030879334"
 ]
}

 The dataset includes 1326 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006968-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8jr9h7
title: Occurrence Download

description: A dataset containing 2595 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1970-2000",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Amaranthus dubius Mart.",
 "TaxonKey is Arachis pietrarellii Krapov. & W.C.Greg.",
 "TaxonKey is Luffa cylindrica (L.) Roem",
 "TaxonKey is Boesenbergia rotunda (L.) Mansf.",
 "TaxonKey is Abelmoschus manihot (L.) Medik.",
 "TaxonKey is Abelmoschus ficulneus (L.) Wight & Arn. ex Wight",
 "TaxonKey is Aegilops speltoides Tausch",
 "TaxonKey is Triticum monococcum L.",
 "TaxonKey is Triticum durum Desf."
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2595 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013460-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpf9qg
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Andrena kaguya Hirashima, 1965)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 78 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278048-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sffrxp
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pitcairnia pruinosa Kunth"
 ]
}

 The dataset includes 47 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001918-160526112335914/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ryupwe
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Uganda",
 "TaxonKey is Hylochoerus meinertzhageni Thomas, 1904"
 ]
}

 The dataset includes 69 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006968-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tance3
title: Occurrence Download

description: A dataset containing 4968 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1970-2000",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Amaranthus dubius Mart.",
 "TaxonKey is Urena lobata L.",
 "TaxonKey is Musa acuminata Colla",
 "TaxonKey is Hibiscus cannabinus L.",
 "TaxonKey is Boesenbergia rotunda (L.) Mansf.",
 "TaxonKey is Hodgsonia heteroclita (Roxb.) Hook.fil. & Thomson",
 "TaxonKey is Triticum urartu Thumanjan ex Gandilyan",
 "TaxonKey is Aegilops tauschii Coss.",
 "TaxonKey is Triticum boeoticum Boiss.",
 "TaxonKey is Triticum dicoccoides (Körnicke) G.Schweinfurth",
 "TaxonKey is Eleusine africana Kenn.-O'Byrne"
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4968 records from 162 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013462-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9nshs7
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Andrena miyamotoi Hirashima, 1964)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 15 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278056-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lcaqnz
title: Occurrence Download

description: A dataset containing 5895 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is China",
 "Country is Mongolia",
 "Country is Korea, Republic of",
 "Country is Korea (Democratic People’s Republic of)",
 "Country is Japan",
 "Country is Viet Nam",
 "Country is Lao People’s Democratic Republic",
 "Country is Cambodia",
 "Country is Myanmar",
 "Country is Thailand",
 "Country is Philippines",
 "Country is Indonesia",
 "Country is Timor-Leste",
 "Country is Malaysia",
 "Country is Brunei Darussalam",
 "Country is Singapore",
 "Country is India",
 "Country is Sri Lanka",
 "Country is Maldives",
 "Country is Nepal",
 "Country is Bhutan",
 "Country is Bangladesh",
 "Country is Pakistan",
 "Country is Kazakhstan",
 "Country is Uzbekistan",
 "Country is Turkmenistan",
 "Country is Kyrgyzstan",
 "Country is Tajikistan",
 "Country is Iran (Islamic Republic of)",
 "Country is Afghanistan",
 "Country is Iraq",
 "Country is Kuwait",
 "Country is Saudi Arabia",
 "Country is Bahrain",
 "Country is Qatar",
 "Country is United Arab Emirates",
 "Country is Oman",
 "Country is Yemen",
 "Country is Syrian Arab Republic",
 "Country is Lebanon",
 "Country is Jordan",
 "Country is Cyprus",
 "Country is Palestine, State of",
 "Country is Israel",
 "Country is Georgia",
 "Country is Armenia",
 "Country is Azerbaijan",
 "Country is Türkiye"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Lysimachia Tourn. ex L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5895 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001918-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ay6zjk
title: Occurrence Download

description: A dataset containing 428 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xanthomixis apperti (Colston, 1972)"
 ]
}

 The dataset includes 428 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0397349-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cuxx9w
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-85.95703 10.83331,-90.79102 9.0153,-91.66992 3.42569,-85.78125 -0.52734,-82.35352 4.47786,-83.14453 8.58102,-85.95703 10.83331))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Stenella attenuata (Gray, 1846)"
 ]
}

 The dataset includes 177 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053914-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10373041
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 2.0 of this repository includes all the data generated for the validation cohort during the revision process.
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.8ronyw
title: Occurrence Download

description: A dataset containing 1637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glareola nordmanni Fischer von Waldheim, 1842",
 "Country is South Africa"
 ]
}

 The dataset includes 1637 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001919-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.6678331
title: Tonsil Atlas: CellRanger outputs

description: Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we provide a comprehensive census of cell types forming the human tonsil by applying single cell transcriptome, epigenome, proteome and adaptive immune repertoire as well as spatial transcriptomics, resulting in an atlas of &gt;357,000 cells. We provide a glossary of 132 annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease, here we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs. The data of our tonsil atlas consists of 5 data modalities: scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics. All of them are produced with different platforms from 10X Genomics and processed wiith different flavours of CellRanger. This repository contains the most important outputs from each CellRanger run of each library.
DOI: 10.15468/dl.scq5py
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Andrena placida Smith, 1853)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278064-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wc3dtd
title: Occurrence Download

description: A dataset containing 627 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hartertula flavoviridis (Hartert, 1924)"
 ]
}

 The dataset includes 627 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0397342-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lqnjo2
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "DatasetKey is FloraCAT: Banco de datos de los cormófitos de Cataluña",
 "DatasetKey is Flora d'Andorra",
 "DatasetKey is CSIC-Real Jardín Botánico-Anthos. Sistema de Información de las Plantas de España"
 ]
 },
 "TaxonKey is Arenaria ligericina Lecoq & Lamotte"
 ]
}

 The dataset includes 66 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013463-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3rwvhd
title: Occurrence Download

description: A dataset containing 1128 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diceros bicornis (Linnaeus, 1758)"
 ]
}

 The dataset includes 1128 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001920-171020152545675/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4mupv
title: Occurrence Download

description: A dataset containing 7722 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Andrena nitida (Müller, 1776))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 7722 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278058-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kobsww
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhagomys rufescens (Thomas, 1886)",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006969-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zf35pb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Andrena salicis Robertson, 1891)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Observation, Specimen)",
 "Year is greater than 1945"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278070-200613084148143/datasets/export for details.
DOI: 10.15468/dl.hrzl2u
title: Occurrence Download

description: A dataset containing 43027 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Asparagus officinalis (Dum) Corb.",
 "TaxonKey is Asparagus officinalis L."
 ]
}

 The dataset includes 43027 records from 368 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001921-170822121629195/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f1wdl3
title: Occurrence Download

description: A dataset containing 571 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "TaxonKey is Barycholos pulcher (Boulenger, 1898)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 571 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006969-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4gzc8h
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Brachyplatys subaeneus (Westwood, 1837)"
 ]
}

 The dataset includes 186 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278060-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.