cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.mvkjm4
title: Occurrence Download

description: A dataset containing 482 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((90 0,180 0,180 90,90 90,90 0))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Reynoutria sachalinensis (F.Schmidt) Nakai"
 ]
}

 The dataset includes 482 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030398-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y4qrur
title: Occurrence Download

description: A dataset containing 8344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Laniarius atrococcineus",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 8344 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074329-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-67295
title: Redemption tidings, vol. 47, nos. 1-46, 7 Jan. - 30 Dec. 1971

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.mxw4bd
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Motacilla flava Linnaeus, 1758",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074980-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qh9j4y
title: Occurrence Download

description: A dataset containing 111374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "TaxonKey is Notropis Rafinesque, 1818"
 ]
}

 The dataset includes 111374 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047404-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-67510
title: Redemption tidings, vol. 48, nos. 1-52, 6 Jan. - 28 Dec. 1972

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.t22hbj
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Philodendron senatocarpium Madison"
 ]
}

 The dataset includes 84 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074340-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-67526
title: Redemption tidings, vol. 48, nos. 1-52, 6 Jan. - 28 Dec. 1972

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.gk24gk
title: Occurrence Download

description: A dataset containing 20988 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ulva lactuca L."
 ]
}

 The dataset includes 20988 records from 234 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055316-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xysy6h
title: Occurrence Download

description: A dataset containing 231 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Siratus cailleti (Petit de la Saussaye, 1856)"
 ]
}

 The dataset includes 231 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099136-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.33mpxz
title: Occurrence Download

description: A dataset containing 813 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-100.7144 20.64934,-81.43257 7.61088,-69.40317 6.49167,-58.79947 12.91832,-58.2356 23.26393,-60.11519 31.43384,-65.37805 36.42149,-77.97132 37.77071,-89.24888 36.72339,-99.39868 27.84069,-100.7144 20.64934))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Grampus griseus (G.Cuvier, 1812)"
 ]
}

 The dataset includes 813 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044510-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-67768
title: Redemption tidings, vol. 48, nos. 1-52, 6 Jan. - 28 Dec. 1972

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.ec7fn5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tringa flavipes (J.F.Gmelin, 1789)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074993-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.62m3md
title: Occurrence Download

description: A dataset containing 7905 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cladophora rupestris (L.) Kütz."
 ]
}

 The dataset includes 7905 records from 134 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055323-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-67726
title: Redemption tidings, vol. 48, nos. 1-52, 6 Jan. - 28 Dec. 1972

description: [description english/roman)] Issued weekly.
DOI: 10.15468/dl.ubyprb
title: Occurrence Download

description: A dataset containing 922 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Saguinus oedipus (Linnaeus, 1758)"
 ]
}

 The dataset includes 922 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044520-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wzv8s6
title: Occurrence Download

description: A dataset containing 53675 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Ricinus communis L."
 ]
}

 The dataset includes 53675 records from 780 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0168561-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ybfnm9
title: Occurrence Download

description: A dataset containing 153109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquila audax (Latham, 1802)",
 "HasCoordinate is True",
 "Year is greater than or equal to 1900",
 "Year is less than or equal to 2021",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False"
 ]
}

 The dataset includes 153109 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010372-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.558w79
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cephalaria zeyheriana Szabó"
 ]
}

 The dataset includes 178 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084721-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rmzb0d
title: Occurrence Download

description: A dataset containing 387539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "TaxonKey is Coleoptera"
 ]
}

 The dataset includes 387539 records from 121 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019425-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8xfz2
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Salvia hilarii Benth."
 ]
}

 The dataset includes 43 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160862-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ne9unx
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex scitula Boott"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084755-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2uf5fn
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alsophila fulgens (C.Chr.) D.S.Conant"
 ]
}

 The dataset includes 122 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140541-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fqjlfz
title: Occurrence Download

description: A dataset containing 701990 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Cyanocitta stelleri (Gmelin, 1788)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 701990 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019426-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4jqqs7
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Youngia rosthornii (Diels) Babc. & Stebbins"
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140540-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10957955
title: Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts

description: Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant phage SVs, and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Strikingly, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.
description: The Chinese Human Gut Virome (CHGV) catalog we established previously (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA007087)  consists of 21,648 non-redundant phage genomes, and was assembled by using a hybrid pipeline that combined both short- (Illumina) and long- (PacBio) reads.
description: Content




PBSV_pipeline.sh: Scripts for detecting phage structural variations across the CHGV cohort

Benchmarking_pipeline.sh: Generating sumulated virome-enriched metagenomics datasets with known introduced SVs and benchmarking different long-read based SV calling methods with PSDP pipeline.

Analysis_script/PhageSV_quality_Part1.R: Overview of 14,438 non-redundant structural variants (SVs) in the human gut phageome.

Analysis_script/Functional_enrichment_analysis.py: Functional enrichment analysis of phage SVs.

Analysis_script/PhageSV_function.R: Visualization of enriched functions in phage SVs.

Analysis_script/PhageSV_GE.R: Bacteria-to-phage HGT analysis

Analysis_script/PhageSV_BVinteraction.R: Bactera-phage SV sharing network

Analysis_script/PhageSV_Phage_host_GE_analysis.R: Phage-host genetical interaction analysis




Data




Results/Sample_SV_common_0.8_suppl.vcf: 14,334 non-redundant VCF file

Results/SV_bed_inf.tsv: Viral SV information extracted from non-redundant VCF file

Results/all_genome_SNP_inf.tsv: SNV for each viral contig extracted from the output file of inStrain

Results/all_gene_SNP_inf.tsv: SNV for each viral gene extracted from the output file of inStrain

ViralSV_density_inf: SV density per viral_contig per sample, taxonomy, Temperate lifestyle
DOI: 10.5281/zenodo.10957956
title: Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts

description: Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant phage SVs, and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Strikingly, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.
description: The Chinese Human Gut Virome (CHGV) catalog we established previously (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA007087)  consists of 21,648 non-redundant phage genomes, and was assembled by using a hybrid pipeline that combined both short- (Illumina) and long- (PacBio) reads.
description: Content




PBSV_pipeline.sh: Scripts for detecting phage structural variations across the CHGV cohort

Benchmarking_pipeline.sh: Generating sumulated virome-enriched metagenomics datasets with known introduced SVs and benchmarking different long-read based SV calling methods with PSDP pipeline.

Analysis_script/PhageSV_quality_Part1.R: Overview of 14,438 non-redundant structural variants (SVs) in the human gut phageome.

Analysis_script/Functional_enrichment_analysis.py: Functional enrichment analysis of phage SVs.

Analysis_script/PhageSV_function.R: Visualization of enriched functions in phage SVs.

Analysis_script/PhageSV_GE.R: Bacteria-to-phage HGT analysis

Analysis_script/PhageSV_BVinteraction.R: Bactera-phage SV sharing network

Analysis_script/PhageSV_Phage_host_GE_analysis.R: Phage-host genetical interaction analysis




Data




Results/Sample_SV_common_0.8_suppl.vcf: 14,334 non-redundant VCF file

Results/SV_bed_inf.tsv: Viral SV information extracted from non-redundant VCF file

Results/all_genome_SNP_inf.tsv: SNV for each viral contig extracted from the output file of inStrain

Results/all_gene_SNP_inf.tsv: SNV for each viral gene extracted from the output file of inStrain

ViralSV_density_inf: SV density per viral_contig per sample, taxonomy, Temperate lifestyle
DOI: 10.15468/dl.cw6pyw
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Atriplex fera (L.) Bunge"
 ]
}

 The dataset includes 161 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0170072-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jev2d3
title: Occurrence Download

description: A dataset containing 58880 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pogonias cromis (Linnaeus, 1766)"
 ]
}

 The dataset includes 58880 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140425-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6zn95f
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Viscum semialatum Lecomte"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140542-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vucxsi
title: Occurrence Download

description: A dataset containing 650 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Rhodanthe laevis (A.Gray) Paul G.Wilson"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 650 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019427-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.43tn3b
title: Occurrence Download

description: A dataset containing 6995799 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 {
 "or" : [
 "License is CC0 1.0",
 "License is CC-BY 4.0",
 "License is CC-BY-NC 4.0"
 ]
 },
 "TaxonKey is Aves"
 ]
}

 The dataset includes 6995799 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0323733-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9hvys7
title: Occurrence Download

description: A dataset containing 532 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Silurus asotus Linnaeus, 1758"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 532 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019429-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98bu3t
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Tagetes erecta L."
 ]
}

 The dataset includes 220 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0181894-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pjt52z
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Myrmecophaga tridactyla Linnaeus, 1758"
 ]
}

 The dataset includes 159 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019429-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n23cjq
title: Occurrence Download

description: A dataset containing 277 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Microlophus jacobii (Baur, 1892)"
 ]
}

 The dataset includes 277 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084691-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.37g82g
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aechmea downsiana Pittendr."
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140545-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cbub2
title: Occurrence Download

description: A dataset containing 246790 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is Fungal Records Database of Britain and Ireland",
 {
 "or" : [
 "Geometry POLYGON((55 13,180 13,180 47,55 47,55 13))",
 "Geometry POLYGON((55 13,180 13,180 90,55 90,55 13))",
 "Geometry POLYGON((-180 13,180 13,180 90,-180 90,-180 13))"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi",
 "Year 2000-2021"
 ]
}

 The dataset includes 246790 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0201573-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ngkjpf
title: Occurrence Download

description: A dataset containing 356737 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Phalaris arundinacea L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 356737 records from 578 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019429-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.