cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12714373
title: eDNAglobe: investigating global organism distribution via environmental DNA metabarcoding data

description: Data generated for eDNAglobe, and codes used to generate the data
description: sample_meta.txt.gz

The meta data for 1,534,010 eDNA samples from which at least one cellular organism (prokaryote or eukaryote) can be identified. It is in TSV format, which contains the following five columns:



Sample ID in NCBI SRA Accession. e.g. DRR023354

Latitude in decimal format. e.g. 38.0367 (Northern hemisphere) or -44.433 (Southern hemisphere)

Longitude in decimal format. e.g. 140.572 (East longitude) or -79.9845 (West longitude)

The barcoding markers of this sample. Might be missing value (\N), or multiple values separated by comma (e.g. ND2,MT16S,MT12S,COX1) indicating multi-barcode sequencing.

Sampling year.


 
description: species_with_DNA.tsv.txt.gz

The 505,842 species included in the reference database (nt_euk and nt_prok) by November 1, 2023. It is in TSV format, which contains the following four columns:



Taxon ID in NCBI Taxonomy Database. e.g. 476039

Number of DNA sequences in the reference database.

Lineage names separated by comma. e.g. Eukaryota;Viridiplantae;Streptophyta;Ranunculales;Ranunculaceae;Thalictroideae;Thalictrum;Thalictrum minus

Lineage ranks eparated by comma. e.g. superkingdom;kingdom;phylum;order;family;subfamily;genus;species


 
description: species_eDNA_GBIF.tsv.txt.gz

The 362,719 species that were both in the reference database and in the GBIF database (by November 1, 2023). It is in TSV format, which contains the following columns:



taxonid_NCBI: Taxon ID in NCBI Taxonomy Database.



taxonid_GBIF: Taxon ID in GBIF Database, might be multiple values separated by comma




main_group: might be: Vertebrates, Invertebrates, Plants, Fungi, Protists, Bacteria, Archaea




sub_group: see definitions at https://edna-globe.k.u-tokyo.ac.jp/help/#help-data-taxonomy.




max_abundance: the max read abundance over all eDNA samples for this species. In value (0~1). Value 0 indicates no detection in any eDNA samples.




is_present_in_eDNA: Yes or No.






is_present_in_GBIF: Yes or No.
description: clean_taxids.txt.gz

a list of 646,743 taxon IDs obtained from the NCBI Taxonomy database accessed on November 1, 2023, using the following criteria: ("species"[Rank] OR "subspecies"[Rank] OR "strain"[Rank] OR "varietas"[Rank]) NOT "uncultured"[Filter] NOT "unclassified"[Filter] NOT "unspecified"[Filter].
description: amplicons.fa.txt & amplicons.blast.xlsx

The denoised amplicon sequences from the metabarcoding data of an eDNA sample from the sediment of seagrass meadows at the New Limassol Port, Cyprus (SRR19858306, https://doi.org/10.3390/d14070549), and the best hit for each sequence against the reference database

 
description: example_for_denoise_and_blast.sh

Scripts used for analyzing SRA data.
DOI: 10.5281/zenodo.12714374
title: eDNAglobe: investigating global organism distribution via environmental DNA metabarcoding data

description: Data generated for eDNAglobe, and codes used to generate the data
description: sample_meta.txt.gz

The meta data for 1,534,010 eDNA samples from which at least one cellular organism (prokaryote or eukaryote) can be identified. It is in TSV format, which contains the following five columns:



Sample ID in NCBI SRA Accession. e.g. DRR023354

Latitude in decimal format. e.g. 38.0367 (Northern hemisphere) or -44.433 (Southern hemisphere)

Longitude in decimal format. e.g. 140.572 (East longitude) or -79.9845 (West longitude)

The barcoding markers of this sample. Might be missing value (\N), or multiple values separated by comma (e.g. ND2,MT16S,MT12S,COX1) indicating multi-barcode sequencing.

Sampling year.


 
description: species_with_DNA.tsv.txt.gz

The 505,842 species included in the reference database (nt_euk and nt_prok) by November 1, 2023. It is in TSV format, which contains the following four columns:



Taxon ID in NCBI Taxonomy Database. e.g. 476039

Number of DNA sequences in the reference database.

Lineage names separated by comma. e.g. Eukaryota;Viridiplantae;Streptophyta;Ranunculales;Ranunculaceae;Thalictroideae;Thalictrum;Thalictrum minus

Lineage ranks eparated by comma. e.g. superkingdom;kingdom;phylum;order;family;subfamily;genus;species


 
description: species_eDNA_GBIF.tsv.txt.gz

The 362,719 species that were both in the reference database and in the GBIF database (by November 1, 2023). It is in TSV format, which contains the following columns:



taxonid_NCBI: Taxon ID in NCBI Taxonomy Database.



taxonid_GBIF: Taxon ID in GBIF Database, might be multiple values separated by comma




main_group: might be: Vertebrates, Invertebrates, Plants, Fungi, Protists, Bacteria, Archaea




sub_group: see definitions at https://edna-globe.k.u-tokyo.ac.jp/help/#help-data-taxonomy.




max_abundance: the max read abundance over all eDNA samples for this species. In value (0~1). Value 0 indicates no detection in any eDNA samples.




is_present_in_eDNA: Yes or No.






is_present_in_GBIF: Yes or No.
description: clean_taxids.txt.gz

a list of 646,743 taxon IDs obtained from the NCBI Taxonomy database accessed on November 1, 2023, using the following criteria: ("species"[Rank] OR "subspecies"[Rank] OR "strain"[Rank] OR "varietas"[Rank]) NOT "uncultured"[Filter] NOT "unclassified"[Filter] NOT "unspecified"[Filter].
description: amplicons.fa.txt & amplicons.blast.xlsx

The denoised amplicon sequences from the metabarcoding data of an eDNA sample from the sediment of seagrass meadows at the New Limassol Port, Cyprus (SRR19858306, https://doi.org/10.3390/d14070549), and the best hit for each sequence against the reference database

 
description: example_for_denoise_and_blast.sh

Scripts used for analyzing SRA data.
DOI: 10.15468/dl.bnxm5n
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyloxalus insulatus (Duellman, 2004)"
 ]
}

 The dataset includes 56 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024162-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.25pvms
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chloroglyphica variegata (Butler, 1889)"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024163-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wq9te
title: Occurrence Download

description: A dataset containing 209 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyloxalus italoi Páez-Vacas, Coloma & Santos, 2010"
 ]
}

 The dataset includes 209 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024164-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aqrhej
title: Occurrence Download

description: A dataset containing 752 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "DatasetKey is EOD – eBird Observation Dataset",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chrysolophus amherstiae (Leadbeater, 1829)",
 "Year 2001-2024"
 ]
}

 The dataset includes 752 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024165-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h2chv6
title: Occurrence Download

description: A dataset containing 7382 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Kostrzyca Forest Gene Bank Database"
 ]
}

 The dataset includes 7382 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024166-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aa55wt
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyloxalus maculosus (Rivero, 1991)"
 ]
}

 The dataset includes 123 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024167-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13804903
title: US-Accidents: A San Francisco Traffic Accident Dataset
DOI: 10.5281/zenodo.13804904
title: US-Accidents: A San Francisco Traffic Accident Dataset
DOI: 10.6084/m9.figshare.27073309
title: Supplementary Material for: Assessing disease control in patients with atopic dermatitis by using the Atopic Dermatitis Control Tool (ADCT) in daily practice

description: Introduction: Atopic dermatitis (AD) is a chronic inflammatory skin disease, placing a significant burden on patients’ quality of life (QoL). The validated Atopic Dermatitis Control Tool (ADCT) is recommended to assess AD control in adults. The aim of this study is to assess AD control and explore associations with demographic characteristics, patient-reported outcome measures (PROMs), and treatment. 
Methods: In this cross-sectional study, questionnaires were sent to 2066 adults from two tertiary referral centers who had previously physician-diagnosed AD and had visited the outpatient clinic at least once between 2020-2022. Questionnaires were completed between May and October 2022. AD control was assessed by the ADCT, with a score ≥7 indicating uncontrolled AD. AD severity, QoL and weekly average pruritus were simultaneously measured using the Patient-Oriented Eczema Measure (POEM), Dermatology Life Quality Index (DLQI), and Numeric Rating Scale (NRS), respectively, with higher scores indicating more severe symptoms. Moreover, treatment-related questions were included. Associations between uncontrolled AD, age, sex and treatment were explored using multivariate logistic regression analysis.
Results: In total, 863 patients (41.8%) filled out the questionnaire and 812 were included in the analysis, of which 59% reported controlled AD. Uncontrolled AD was associated with higher PROMs scores and receiving topical anti-inflammatories only (adjusted odds ratio (95% confidence interval) ranged from 1.33 (0.995-1.88) to 2.55 (2.21-2.86)). Of those treated with topical anti-inflammatories only, 54% reported uncontrolled AD.
Conclusion: The majority of the patients reported controlled AD. Patients with uncontrolled AD often reported more severe symptoms and were more likely to receive topical anti-inflammatories only. It could be considered to shift patients with uncontrolled AD from topical to systemic treatment.
DOI: 10.15468/dl.7ptgxn
title: Occurrence Download

description: A dataset containing 168160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "PublishingOrg is a2fa5b68-3ebf-4845-abc5-f456d251386f",
 "Year 2004-2024"
 ]
}

 The dataset includes 168160 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024160-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jce4ka
title: Occurrence Download

description: A dataset containing 5087900 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Year 2010-2024"
 ]
}

 The dataset includes 5087900 records from 3074 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024158-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kt5ae4
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Elatine brachysperma A.Gray",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 30 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175282-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qpnhss
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Agave pintilla S.González, M.González & L.Reséndiz"
 ]
}

 The dataset includes 34 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0141586-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qmwpeb
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Goniothalamus gigantifolius Merr."
 ]
}

 The dataset includes 12 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016935-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.twqowp
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Quesnelia marmorata (Lem.) Read",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021511-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y4u6qr
title: Occurrence Download

description: A dataset containing 77551 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Odocoileus virginianus (Zimmermann, 1780)"
 ]
}

 The dataset includes 77551 records from 237 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0182334-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bproju
title: Occurrence Download

description: A dataset containing 12523 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microtus ochrogaster (Wagner, 1842)"
 ]
}

 The dataset includes 12523 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021512-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dtqqha
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hedyotis verticillaris Wall. ex Wight & Arn."
 ]
}

 The dataset includes 51 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016936-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vx3wzd
title: Occurrence Download

description: A dataset containing 11037 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zalophus californianus (Lesson, 1828)"
 ]
}

 The dataset includes 11037 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0186818-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tcjdt1
title: Occurrence Download

description: A dataset containing 1174 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microtus pinetorum scalopsoides"
 ]
}

 The dataset includes 1174 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021513-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xr79qy
title: Occurrence Download

description: A dataset containing 963 species occurrences available in GBIF matching the query:
{
 "SpeciesKey" : [
 "is Amanita franchetii (Boud.) Fayod"
 ]
}

 The dataset includes 963 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0150322-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e7bpjz
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gutenbergia gilbertii C.Jeffrey"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016948-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dkwl3f
title: Occurrence Download

description: A dataset containing 490511 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Human Observation"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Proteaceae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 490511 records from 304 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021514-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnp45c
title: Occurrence Download

description: A dataset containing 104352 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gammaridae",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than 2000"
 ]
}

 The dataset includes 104352 records from 401 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163523-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2vj9gc
title: Occurrence Download

description: A dataset containing 657 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Subeucalanus monachus (Giesbrecht, 1888)"
 ]
}

 The dataset includes 657 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0141588-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qpbva5
title: Occurrence Download

description: A dataset containing 695 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hesperantha radiata (Jacq.) Ker Gawl."
 ]
}

 The dataset includes 695 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021909-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dumghv
title: Occurrence Download

description: A dataset containing 211 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acaena argentea Ruiz & Pav."
 ]
}

 The dataset includes 211 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163494-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6kjnue
title: Occurrence Download

description: A dataset containing 23256 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microtus longicaudus (Merriam, 1888)"
 ]
}

 The dataset includes 23256 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021514-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mxqa65
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Horsfieldia urceolata W.J.de Wilde"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021910-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nvbj9a
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Elatine minima (Nutt.) Fisch. & C.A.Mey.",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Continent is North America"
 ]
}

 The dataset includes 124 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175283-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.iu22l6
title: Occurrence Download

description: A dataset containing 98076 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-39.88599 -52.86118,-39.71018 -56.32188,-33.11746 -56.3706,-33.0735 -52.8877,-39.88599 -52.86118))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 98076 records from 139 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021515-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpwsn9
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Horsfieldia xanthina Airy Shaw"
 ]
}

 The dataset includes 18 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021934-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t7j52q
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Androsace cylindrica subsp. willkommii P.Monts."
 ]
}

 The dataset includes 61 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0163521-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r72wh1
title: Occurrence Download

description: A dataset containing 164 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "TaxonKey is Cecropia glaziovii Snethl.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 164 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021517-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.