cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.bsd9hu
title: Occurrence Download

description: A dataset containing 937 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bactrocera invadens Drew, Tsuruta & White, 2005"
 ]
}

 The dataset includes 937 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013859-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4fkhha
title: Occurrence Download

description: A dataset containing 3786 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((119.72602 19.85382,133.79454 19.85382,133.79454 25.47882,119.72602 25.47882,119.72602 19.85382))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Melastomataceae"
 ]
}

 The dataset includes 3786 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0270811-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5zu7b2
title: Occurrence Download

description: A dataset containing 289 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllodactylus angustidigitus Dixon & Huey, 1970"
 ]
}

 The dataset includes 289 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006465-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mxauw8
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.29801 10.25177,-74.65084 10.25177,-74.65084 11.18832,-75.29801 11.18832,-75.29801 10.25177))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Saguinus oedipus (Linnaeus, 1758)"
 ]
}

 The dataset includes 134 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006466-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15107241
title: Toy input dataset for "snrnaseq-step5-process-dea-results" code, from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667)

description: This is a toy dataset that can be used to run code step #5 from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667), which identifies k-fold cross-validated DEGs and DEG subclusters resulting from differential expression analysis of single-nucleus RNA sequencing data (Github: https://github.com/amwilson149/snrnaseq-step5-process-dea-results/tree/main).

To test the code on this dataset, place these files in the 'data' directory of the code repository, and unzip the compressed files. Then run the script.

 

A description of the study using this code follows:

For people with HIV (PWH), substance use disorders (SUDs) are a prominent neurological risk factor, and the impacts of both on dopaminergic pathways are a potential point of deleterious convergence. Here, we profile, at single nucleus resolution, the substantia nigra (SN) transcriptomes of 90 postmortem donors in the context of chronic HIV and opioid/cocaine SUD, including 67 prospectively characterized PWH. We report altered microglial expression for hundreds of pro- and anti-inflammatory regulators attributable to HIV, and separately, to SUD. Stepwise, progressive microglial dysregulation, coupled to altered SN dopaminergic and GABAergic signaling, was associated with SUD/HIV dual diagnosis and further with lack of viral suppression in blood. In virologically suppressed donors, SUD comorbidity was associated with microglial transcriptional changes permissive for HIV infection. We report HIV-related downregulation of monoamine reuptake transporters specifically in dopaminergic neurons regardless of SUD status or viral load, and additional transcriptional signatures consistent with selective vulnerability of SN dopamine neurons.
description: The input data for DEG subclustering that is stored here includes real DEG lists, but heavily downsampled expression data. As a result, some of the DEGs drop out of coordinated DEG subcluster identification (because their expression data was removed in the toy dataset). This looks like white/empty rows/columns in DEG correlation matrices.
DOI: 10.5281/zenodo.15107242
title: Toy input dataset for "snrnaseq-step5-process-dea-results" code, from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667)

description: This is a toy dataset that can be used to run code step #5 from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667), which identifies k-fold cross-validated DEGs and DEG subclusters resulting from differential expression analysis of single-nucleus RNA sequencing data (Github: https://github.com/amwilson149/snrnaseq-step5-process-dea-results/tree/main).

To test the code on this dataset, place these files in the 'data' directory of the code repository, and unzip the compressed files. Then run the script.

 

A description of the study using this code follows:

For people with HIV (PWH), substance use disorders (SUDs) are a prominent neurological risk factor, and the impacts of both on dopaminergic pathways are a potential point of deleterious convergence. Here, we profile, at single nucleus resolution, the substantia nigra (SN) transcriptomes of 90 postmortem donors in the context of chronic HIV and opioid/cocaine SUD, including 67 prospectively characterized PWH. We report altered microglial expression for hundreds of pro- and anti-inflammatory regulators attributable to HIV, and separately, to SUD. Stepwise, progressive microglial dysregulation, coupled to altered SN dopaminergic and GABAergic signaling, was associated with SUD/HIV dual diagnosis and further with lack of viral suppression in blood. In virologically suppressed donors, SUD comorbidity was associated with microglial transcriptional changes permissive for HIV infection. We report HIV-related downregulation of monoamine reuptake transporters specifically in dopaminergic neurons regardless of SUD status or viral load, and additional transcriptional signatures consistent with selective vulnerability of SN dopamine neurons.
description: The input data for DEG subclustering that is stored here includes real DEG lists, but heavily downsampled expression data. As a result, some of the DEGs drop out of coordinated DEG subcluster identification (because their expression data was removed in the toy dataset). This looks like white/empty rows/columns in DEG correlation matrices.
DOI: 10.15468/dl.j94sxa
title: Occurrence Download

description: A dataset containing 67639277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Living Specimen, Occurrence evidence)",
 "Geometry POLYGON((-130.15591 51.90972,-131.38659 50.37138,-128.92524 42.52585,-124.31023 30.83447,-93.71234 23.40675,-79.78126 24.07558,-76.07156 27.88834,-69.68261 37.47175,-65.0565 48.65246,-81.32697 48.18868,-104.16784 52.34478,-130.15591 51.90972))",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Ciconia nigra (Linnaeus, 1758), Ciconia ciconia (Linnaeus, 1758), Chroicocephalus ridibundus (Linnaeus, 1766), Chlorocichla flaviventris (A.Smith, 1834), Chiroxiphia caudata (Shaw, 1793), Chen rossii (Cassin, 1861), Chen caerulescens (Linnaeus, 1758), Charadrius vociferus Linnaeus, 1758, Chalcophaps indica (Linnaeus, 1758), Chaetura pelagica (Linnaeus, 1758), Cercomela fusca (Blyth, 1851), Centropus superciliosus Hemprich & Ehrenberg, 1829, Centropus sinensis (Stephens, 1815), Catharus guttatus (Pallas, 1811), Cathartes aura (Linnaeus, 1758), Cariama cristata (Linnaeus, 1766), Carduelis chloris (Linnaeus, 1758), Carduelis carduelis (Linnaeus, 1758), Carduelis cannabina (Linnaeus, 1758), Cardinalis cardinalis (Linnaeus, 1758), Caracara plancus (J.F.Miller, 1777), Caprimulgus fossii Hartlaub, 1857, Cantorchilus modestus (Cabanis, 1861), Butorides striata (Linnaeus, 1758), Buteo swainsoni Bonaparte, 1838, Buteo rufinus (Cretzschmar, 1829), Buteo regalis (G.R.Gray, 1844), Buteo platypterus (Vieillot, 1823), Buteo lineatus (Gmelin, 1788), Buteo lagopus (Pontoppidan, 1763), Buteo jamaicensis (Gmelin, 1788), Buteo buteo (Linnaeus, 1758))",
 "Year 2000-2025"
 ]
}

 The dataset includes 67639277 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006453-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mb665m
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "Locality is one of (buriticá, antioquia, co (6.694, -75.898))"
 ]
}

 The dataset includes 37 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006467-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trwmq5
title: Occurrence Download

description: A dataset containing 343133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Capreolus capreolus (Linnaeus, 1758)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 343133 records from 670 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006462-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s32ff6
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Capricornis swinhoei Gray, 1862",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 86 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006468-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vpymye
title: Occurrence Download

description: A dataset containing 6490 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lindheimera texana A.Gray"
 ]
}

 The dataset includes 6490 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006469-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x93jns
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cephalophus dorsalis Gray, 1846",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 23 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006470-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ju2qyd
title: Occurrence Download

description: A dataset containing 234 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 Rhus chinensis Mill."
 ]
}

 The dataset includes 234 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006473-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kh9xgm
title: Occurrence Download

description: A dataset containing 1076 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dalea compacta Spreng."
 ]
}

 The dataset includes 1076 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006474-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9fvxjs
title: Occurrence Download

description: A dataset containing 12295 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Steatornithiformes"
 ]
}

 The dataset includes 12295 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006475-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3n8fc6
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cephalophus natalensis A.Smith, 1834",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 45 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006478-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p3zsjb
title: Occurrence Download

description: A dataset containing 5733 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Small Mammal Research Database"
 ]
}

 The dataset includes 5733 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006479-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/11211429
title: Micro Gas Turbine Electrical Energy Prediction
DOI: 10.15468/dl.5w9p87
title: Occurrence Download

description: A dataset containing 126469 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nyctibiiformes"
 ]
}

 The dataset includes 126469 records from 344 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006476-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.47sxj3
title: Occurrence Download

description: A dataset containing 156 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 Trachelospermum jasminoides (Lindl.) Lem."
 ]
}

 The dataset includes 156 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006481-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hpt6p3
title: Occurrence Download

description: A dataset containing 54 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 Pinellia pedatisecta Schott"
 ]
}

 The dataset includes 54 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006482-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9x69yf
title: Occurrence Download

description: A dataset containing 28641695 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gruiformes"
 ]
}

 The dataset includes 28641695 records from 5404 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006471-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.95q47x
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "TaxonKey is Amanita flavipes S.Imai"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0147731-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mhyjmh
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Lychnophora nanuzae Semir",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 18 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034303-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f9bqn9
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gaultheria undata (J.J.Sm.) Kron & P.W.Fritsch"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010578-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.soc8m1
title: Occurrence Download

description: A dataset containing 614 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Opuntia dillenii (Ker Gawl.) Haw.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 614 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034303-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cjvsej
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scleria parallella C.B.Clarke"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180835-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kt4wuf
title: Occurrence Download

description: A dataset containing 6347 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "StateProvince is one of (meta)",
 "TaxonKey is one of (Crocodylia, Squamata, Testudines)"
 ]
 }
 ]
}

 The dataset includes 6347 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017811-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ypgps
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation"
 ]
 },
 "CoordinateUncertaintyInMeters 0.0-1000000.0",
 "Country is United States of America",
 "GadmGid is USA.32_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Gymnorhinus cyanocephalus Wied-Neuwied, 1841"
 ]
}

 The dataset includes 29 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0158357-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxa7ky
title: Occurrence Download

description: A dataset containing 12837 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "TaxonKey is Balaenoptera physalus (Linnaeus, 1758)"
 ]
}

 The dataset includes 12837 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034304-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pxdern
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bromheadia humilis Kruiz. & de Vogel"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076621-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.um784c
title: Occurrence Download

description: A dataset containing 323307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mollusca"
 ]
}

 The dataset includes 323307 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0147732-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7v7f6v
title: Occurrence Download

description: A dataset containing 59034 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-97.0752 46.66339,-96.44897 46.66339,-96.44897 46.99412,-97.0752 46.99412,-97.0752 46.66339))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 59034 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034305-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rj6wcr
title: Occurrence Download

description: A dataset containing 349 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gagea commutata K.Koch"
 ]
}

 The dataset includes 349 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003875-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.