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

description: A dataset containing 56555 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "Country is Canada",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Caudata"
 ]
}

 The dataset includes 56555 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004822-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8303455
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Franz Martin Hilgendorf, http://www.wikidata.org/entity/Q105603. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q105603
DOI: 10.5281/zenodo.18716534
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Gustaaf Adolf Frederik Molengraaff, http://www.wikidata.org/entity/Q1255637. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q1255637
DOI: 10.5281/zenodo.18750958
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Gustaaf Adolf Frederik Molengraaff, http://www.wikidata.org/entity/Q1255637. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q1255637
DOI: 10.5281/zenodo.18718140
title: Longitudinal blood transcriptome profiling reveals immune dynamics in sepsis: Raw RNA-seq FASTQ files

description: This dataset contains raw RNA-seq FASTQ files from a longitudinal blood transcriptomic study of sepsis and septic shock patients.


Study Summary: Serial whole-blood samples were collected from 11 adult patients (5 sepsis, 6 septic shock) and 4 healthy controls enrolled at the Korea University Ansan Hospital. Blood draws were performed on hospital day 1 (HD#1), day 3 (HD#3), and day 7 (HD#7) using PAXgene tubes. RNA was extracted and sequenced on Illumina NovaSeq X Plus (2×100 bp paired-end) after rRNA depletion using TruSeq Stranded Total RNA Library Prep Globin kit. This study identified a neutrophil-driven transcriptomic signature that reflects early hyperinflammatory responses in sepsis, tracks disease severity and temporal progression, and predicts 28-day mortality across multiple external cohorts.


File Naming Convention:


  
NC{n}_{read}.fastq.gz — Healthy control samples (n = 0–3; read = 1 or 2 for paired-end)
  
sepsis{patient}_{timepoint}_{read}.fastq.gz — Sepsis patients (patient = 0–4; timepoint = 1/2/3 for HD#1/3/7; read = 1 or 2)
  
septic-shock{patient}_{timepoint}_{read}.fastq.gz — Septic shock patients (patient = 00, 0–4; timepoint = 1/2/3 for HD#1/3/7; read = 1 or 2)



Dataset Contents:


  
4 healthy controls (NC0–NC3): 8 FASTQ files
  
5 sepsis patients (sepsis0–sepsis4), 3 timepoints each: 30 FASTQ files
  
6 septic shock patients (septic-shock00, septic-shock0–septic-shock4), up to 3 timepoints: 32 FASTQ files
  
Total: 70 paired-end FASTQ files



Ethics: The study protocol was approved by the institutional review board of the Korea University Ansan Hospital (IRB No. 2024AS0030). Written informed consent was obtained from study participants or their legal representatives.


Associated manuscript: Hwang J, Cha JH, et al. "Longitudinal blood transcriptome profiling reveals immune dynamics in sepsis." BMC Infectious Diseases (submitted).
description: Funding: This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (RS-2025-00563782, RS-2023-00220894) to Dae Won Park. Sequencing was performed at Macrogen, Seoul, Korea.
DOI: 10.5281/zenodo.18718141
title: Longitudinal blood transcriptome profiling reveals immune dynamics in sepsis: Raw RNA-seq FASTQ files

description: This dataset contains raw RNA-seq FASTQ files from a longitudinal blood transcriptomic study of sepsis and septic shock patients.


Study Summary: Serial whole-blood samples were collected from 11 adult patients (5 sepsis, 6 septic shock) and 4 healthy controls enrolled at the Korea University Ansan Hospital. Blood draws were performed on hospital day 1 (HD#1), day 3 (HD#3), and day 7 (HD#7) using PAXgene tubes. RNA was extracted and sequenced on Illumina NovaSeq X Plus (2×100 bp paired-end) after rRNA depletion using TruSeq Stranded Total RNA Library Prep Globin kit. This study identified a neutrophil-driven transcriptomic signature that reflects early hyperinflammatory responses in sepsis, tracks disease severity and temporal progression, and predicts 28-day mortality across multiple external cohorts.


File Naming Convention:


  
NC{n}_{read}.fastq.gz — Healthy control samples (n = 0–3; read = 1 or 2 for paired-end)
  
sepsis{patient}_{timepoint}_{read}.fastq.gz — Sepsis patients (patient = 0–4; timepoint = 1/2/3 for HD#1/3/7; read = 1 or 2)
  
septic-shock{patient}_{timepoint}_{read}.fastq.gz — Septic shock patients (patient = 00, 0–4; timepoint = 1/2/3 for HD#1/3/7; read = 1 or 2)



Dataset Contents:


  
4 healthy controls (NC0–NC3): 8 FASTQ files
  
5 sepsis patients (sepsis0–sepsis4), 3 timepoints each: 30 FASTQ files
  
6 septic shock patients (septic-shock00, septic-shock0–septic-shock4), up to 3 timepoints: 32 FASTQ files
  
Total: 70 paired-end FASTQ files



Ethics: The study protocol was approved by the institutional review board of the Korea University Ansan Hospital (IRB No. 2024AS0030). Written informed consent was obtained from study participants or their legal representatives.


Associated manuscript: Hwang J, Cha JH, et al. "Longitudinal blood transcriptome profiling reveals immune dynamics in sepsis." BMC Infectious Diseases (submitted).
description: Funding: This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (RS-2025-00563782, RS-2023-00220894) to Dae Won Park. Sequencing was performed at Macrogen, Seoul, Korea.
DOI: 10.5281/zenodo.18750943
title: SCHOOLS

description: SCOOLS RESEARCH
DOI: 10.5281/zenodo.18750942
title: SCHOOLS

description: SCOOLS RESEARCH
DOI: 10.15468/dl.z38d2w
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "TaxonKey is Sardinella tawilis"
 ]
}

 The dataset includes 32 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004877-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aacwt2
title: Occurrence Download

description: A dataset containing 1743 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centruroides edwardsii",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1743 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004874-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wzehua
title: Occurrence Download

description: A dataset containing 8864 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tetragonisca angustula)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8864 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004876-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18750950
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by D. Elmo Hardy, http://www.wikidata.org/entity/Q5203576. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q5203576
DOI: 10.5281/zenodo.8151383
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by D. Elmo Hardy, http://www.wikidata.org/entity/Q5203576. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q5203576
DOI: 10.15468/dl.vjztny
title: Occurrence Download

description: A dataset containing 1198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ambrosia psilostachya",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 1198 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004875-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mym27f
title: Occurrence Download

description: A dataset containing 378853 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is one of (Aponogeton distachyos, Arthurdendyus triangulatus, Cabomba caroliniana, Callosciurus finlaysonii, Cherax destructor, Corvus splendens, Crassula helmsii, Elodea densa, Eriocheir sinensis, Erythranthe guttata, Faxonius immunis, Faxonius juvenilis, Faxonius rusticus, Faxonius virilis, Gambusia affinis, Heracleum mantegazzianum, Heracleum persicum, Heracleum pubescens, Houttuynia cordata, , Impatiens glandulifera, Koenigia polystachya, Lagarosiphon major, Lepomis gibbosus, Limnoperna fortunei, Ludwigia grandiflora, Ludwigia peploides, Lysichiton americanus, Morone americana, Muntiacus reevesi, Myriophyllum aquaticum, Myriophyllum heterophyllum, Pacifastacus leniusculus, Petasites japonicus, Pontederia cordata, Procambarus acutus, Procambarus clarkii, Procambarus virginalis, Pseudorasbora parva, Pycnonotus cafer, Saururus cernuus, Sciurus carolinensis, Sciurus niger, Solenopsis invicta, Solenopsis richteri, Threskiornis aethiopicus, Vespa velutina, Zizania latifolia)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 378853 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004791-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18750955
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Franz Martin Hilgendorf, http://www.wikidata.org/entity/Q105603. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q105603
DOI: 10.15468/dl.yz2aw4
title: Occurrence Download

description: A dataset containing 193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ceratinia tutia",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 193 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004878-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z93y5p
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ambrosia tenuifolia",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 90 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004879-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqqtzp
title: Occurrence Download

description: A dataset containing 353 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "DistanceFromCentroidInMeters is greater than or equal to 2000",
 "TaxonKey is Sardinella zunasi"
 ]
}

 The dataset includes 353 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004880-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c56970b70
title: MassIVE MSV000100941 - Fraction screening post-HPLC for purification of metabolites
title: This dataset simply looks at various fractions pulled from an HPLC run to separate metabolites and find fraction(s) that contain our metallophore(s) of interest. In preparation for sending fractions for 21 T FT-ICR analysis.
DOI: 10.15468/dl.5umz2g
title: Occurrence Download

description: A dataset containing 368 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Specimen)",
 "Geometry POLYGON((-78.43237 32.5268,-123.70508 39.78426,-106.42542 7.64408,-84.30747 -8.94438,-78.77798 0.73223,-66.33662 14.21036,-78.43237 32.5268))",
 "TaxonKey is Agouti paca"
 ]
}

 The dataset includes 368 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004882-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j4knha
title: Occurrence Download

description: A dataset containing 405 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ceratophrys calcarata",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 405 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004883-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kgkxw3
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Amorpha canescens",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 408 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004884-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17841649
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Howard K. Gloyd, http://www.wikidata.org/entity/Q3141570. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q3141570
DOI: 10.5281/zenodo.18750964
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Howard K. Gloyd, http://www.wikidata.org/entity/Q3141570. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q3141570
DOI: 10.5281/zenodo.18102042
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Ronald W. Hodges, http://www.wikidata.org/entity/Q21337810. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21337810
DOI: 10.5281/zenodo.18750970
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Ronald W. Hodges, http://www.wikidata.org/entity/Q21337810. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21337810
DOI: 10.15468/dl.ucsxmv
title: Occurrence Download

description: A dataset containing 1416 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Harpia harpyja",
 "Year 2004-2023"
 ]
}

 The dataset includes 1416 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004886-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7y6nc
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Ampelopsis arborea",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004887-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18750988
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Vladimír Krist, http://www.wikidata.org/entity/Q21517940. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21517940
DOI: 10.5281/zenodo.8067546
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Vladimír Krist, http://www.wikidata.org/entity/Q21517940. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21517940
DOI: 10.15468/dl.gafqx6
title: Occurrence Download

description: A dataset containing 419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cercosaura argulus",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 419 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004888-260221153910048/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24431/rw1k7cx
title: CastAway CTD Data: 2017-2019 and 2021-2024, Gulf Watch Alaska Pelagic Component, Long-term Monitoring of Humpback Whale Predation on Pacific Herring in Prince William Sound

description: These data are part of the Gulf Watch Alaska (GWA) Pelagic component, which is a long-term ecosystem monitoring program of the Exxon Valdez Oil Spill Trustee Council (EVOSTC) for the marine ecosystem affected by the 1989 oil spill. As part of a larger study of humpback whale (Megaptera novaeangliae) impact to Pacific herring (Clupea pallasi) populations in Prince William Sound (PWS), CTD surveys were conducted as part of an integrated fall/winter predator-prey survey. 

Vessel surveys in Prince William Sound (PWS) were conducted twice per year during the spring and fall months to record Conductivity, Temperature, and Depth (CTD) measurements. The surveys were timed to coincide with the movement of whales into the PWS. The surveys visited PWS bays that have historically been used by whales and herring to maintain ongoing EVOSTC funded long term monitoring surveys for humpback whales.

The dataset is presented as .zip file containing collections of CSV files by study year from 2017-2019 and 2021-2024 for different survey locations. A field season in 2020 was cancelled due to the COVID-19 pandemic. The individual CTD files are named: __&lt; Cast time in UTC &gt; location . The files contain pressure, depth, temperature, conductivity, conductance, salinity, sound velocity, and density for each CTD cast. Instrument metadata is contained in the header file.