cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.e3b6x8
title: Occurrence Download

description: A dataset containing 1636 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-80.14960 -1.50445,-73.11526 -1.50445,-73.11526 1.30805,-80.14960 1.30805,-80.14960 -1.50445))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Odocoileus virginianus (Zimmermann, 1780)"
 ]
}

 The dataset includes 1636 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021152-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bp7hgb
title: Occurrence Download

description: A dataset containing 4192020 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guatemala",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4192020 records from 1367 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005283-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.msbttr
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Borbo borbonica (Boisduval, 1833)",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 35 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019363-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j8cx8m
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Goniothalamus majestatis Kessler"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017042-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.buedal
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Borbo borbonica (Boisduval, 1833)",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 35 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019364-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kj9s8b
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-28.87027 26.47579,63.87027 26.47579,63.87027 63.52421,-28.87027 63.52421,-28.87027 26.47579))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Thaumetopoea processionea Linnaeus, 1758"
 ]
}

 The dataset's 4 records were derived from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024167-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjr5rv
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helicia fuscotomentosa Suess."
 ]
}

 The dataset includes 68 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017018-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b9kukf
title: Occurrence Download

description: A dataset containing 15159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "FamilyKey is Staphylinidae",
 "Country is Italy"
 ]
}

 The dataset includes 15159 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005293-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9uuw5z
title: Occurrence Download

description: A dataset containing 251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Otomys angoniensis Wroughton, 1906",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 251 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033999-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15634534
title: АНАТОМИЧЕСКОЕ СТРОЕНИЕ АССИМИЛИРУЮЩИХ ОРГАНОВ ERUCA SATIVA MILL. (СЕМ.BRASSICACEAE) ПРИ  ИНТРОДУКЦИИ В СУРХАНДАРЬИНСКОЙ ОБЛАСТИ
DOI: 10.5281/zenodo.15634535
title: АНАТОМИЧЕСКОЕ СТРОЕНИЕ АССИМИЛИРУЮЩИХ ОРГАНОВ ERUCA SATIVA MILL. (СЕМ.BRASSICACEAE) ПРИ  ИНТРОДУКЦИИ В СУРХАНДАРЬИНСКОЙ ОБЛАСТИ
DOI: 10.5281/zenodo.12668041
title: Data for methylome sequencing: Enriching and Profiling Methylomes for Tumor Classification and Liquid Biopsies

description: We benchmarked and demonstrated the versatility of FLEXseq (Fragment Ligation EXclusive methylation sequencing) across different sample types: genomic DNA from the K562 (leukemia) cell line, DNA mix-in titrations of four immune cell types (B cells, T cells, monocytes, and neutrophils), DNA titrations of three cancer cell lines (breast invasive carcinoma [BRCA], colon adenocarcinoma [COAD], and glioblastoma [GBM]) mixed with those four immune cell mixtures separately, input titrations of cell-free (cf) DNA from one plasma sample and DNA from formalin-fixed paraffin-embedded (FFPE) tissues, cfDNA from 106 cerebrospinal fluids (CSF) and 42 other body fluids, and DNA from 37 FFPE tissues.

We sequenced all the samples mentioned above using FLEXseq. Paired-end reads were quality and length trimmed with cutadapt version 3.5, and all high-quality sequencing reads were then aligned to the hg38 reference genome using Bismark v0.23.0. We then filtered out reads with unmethylated cytosine in the non-CpG context with filter_non_conversion function. Next, we used the bismark_methylation_extractor function to extract the methylation calls (removing single-nucleotide polymorphisms [SNP]).

We also used the bam2pat function from wgbs_tools, to convert bam files into .pat files for deconvolution, keeping reads covering at least three CpG sites. The .pat files preserve fragment-level data and were de-identified by removing SNPs using the mask_pat function. 

We used CNVkit (v0.9.1) to analyze and visualize genome-wide copy numbers. Our inputs into CNVkit were Bismark/Bowtie 2 aligned BAM files that were deduplicated by Bismark based on end positions and fragment lengths. We then generated log2copy ratio plots for all body fluid and FFPE samples based on the pooled reference and visualized them across all bins using the DNAcopy R package.

We used t-distributed stochastic neighbor embedding (t-SNE) dimensionality reduction to visualize the embedding of our method cases using the TCGA and CNS tumor references. For the CNS tumor t-SNE plots, 2,801 references were used. We extracted 94 nontrivial components using the RSpectra R package and then employed the Rtsne R package with parameters of ‘pca=F, max_iter=2500, theta=0, perplexity=30’. For the TCGA t-SNE plots, 2,508 references were used with the same parameters above. Individual samples were incorporated separately into the references.
DOI: 10.5281/zenodo.13931578
title: Data for methylome sequencing: Enriching and Profiling Methylomes for Tumor Classification and Liquid Biopsies

description: We benchmarked and demonstrated the versatility of FLEXseq (Fragment Ligation EXclusive methylation sequencing) across different sample types: genomic DNA from the K562 (leukemia) cell line, DNA mix-in titrations of four immune cell types (B cells, T cells, monocytes, and neutrophils), DNA titrations of three cancer cell lines (breast invasive carcinoma [BRCA], colon adenocarcinoma [COAD], and glioblastoma [GBM]) mixed with those four immune cell mixtures separately, input titrations of cell-free (cf) DNA from one plasma sample and DNA from formalin-fixed paraffin-embedded (FFPE) tissues, cfDNA from 106 cerebrospinal fluids (CSF) and 42 other body fluids, and DNA from 37 FFPE tissues.

We sequenced all the samples mentioned above using FLEXseq. Paired-end reads were quality and length trimmed with cutadapt version 3.5, and all high-quality sequencing reads were then aligned to the hg38 reference genome using Bismark v0.23.0. We then filtered out reads with unmethylated cytosine in the non-CpG context with filter_non_conversion function. Next, we used the bismark_methylation_extractor function to extract the methylation calls (removing single-nucleotide polymorphisms [SNP]).

We also used the bam2pat function from wgbs_tools, to convert bam files into .pat files for deconvolution, keeping reads covering at least three CpG sites. The .pat files preserve fragment-level data and were de-identified by removing SNPs using the mask_pat function. 

We used CNVkit (v0.9.1) to analyze and visualize genome-wide copy numbers. Our inputs into CNVkit were Bismark/Bowtie 2 aligned BAM files that were deduplicated by Bismark based on end positions and fragment lengths. We then generated log2copy ratio plots for all body fluid and FFPE samples based on the pooled reference and visualized them across all bins using the DNAcopy R package.

We used t-distributed stochastic neighbor embedding (t-SNE) dimensionality reduction to visualize the embedding of our method cases using the TCGA and CNS tumor references. For the CNS tumor t-SNE plots, 2,801 references were used. We extracted 94 nontrivial components using the RSpectra R package and then employed the Rtsne R package with parameters of ‘pca=F, max_iter=2500, theta=0, perplexity=30’. For the TCGA t-SNE plots, 2,508 references were used with the same parameters above. Individual samples were incorporated separately into the references.
DOI: 10.5281/zenodo.14606089
title: Data for methylome sequencing: Enriching and Profiling Methylomes for Tumor Classification and Liquid Biopsies

description: We benchmarked and demonstrated the versatility of FLEXseq (Fragment Ligation EXclusive methylation sequencing) across different sample types: genomic DNA from the K562 (leukemia) cell line, DNA mix-in titrations of four immune cell types (B cells, T cells, monocytes, and neutrophils), DNA titrations of three cancer cell lines (breast invasive carcinoma [BRCA], colon adenocarcinoma [COAD], and glioblastoma [GBM]) mixed with those four immune cell mixtures separately, input titrations of cell-free (cf) DNA from one plasma sample and DNA from formalin-fixed paraffin-embedded (FFPE) tissues, cfDNA from 106 cerebrospinal fluids (CSF) and 42 other body fluids, and DNA from 37 FFPE tissues.

We sequenced all the samples mentioned above using FLEXseq. Paired-end reads were quality and length trimmed with cutadapt version 3.5, and all high-quality sequencing reads were then aligned to the hg38 reference genome using Bismark v0.23.0. We then filtered out reads with unmethylated cytosine in the non-CpG context with filter_non_conversion function. Next, we used the bismark_methylation_extractor function to extract the methylation calls (removing single-nucleotide polymorphisms [SNP]).

We also used the bam2pat function from wgbs_tools, to convert bam files into .pat files for deconvolution, keeping reads covering at least three CpG sites. The .pat files preserve fragment-level data and were de-identified by removing SNPs using the mask_pat function. 

We used CNVkit (v0.9.10) to analyze and visualize genome-wide copy numbers. Our inputs into CNVkit were Bismark/Bowtie 2 aligned BAM files deduplicated by Bismark based on end positions and fragment lengths. We then generated log2copy ratio plots for all body fluid and FFPE samples based on the pooled reference and visualized them across all bins using the DNAcopy R package.
DOI: 10.5281/zenodo.12668040
title: Data for methylome sequencing: Enriching and Profiling Methylomes for Tumor Classification and Liquid Biopsies

description: We benchmarked and demonstrated the versatility of FLEXseq (Fragment Ligation EXclusive methylation sequencing) across different sample types: genomic DNA from the K562 (leukemia) cell line, DNA mix-in titrations of four immune cell types (B cells, T cells, monocytes, and neutrophils), DNA titrations of three cancer cell lines (breast invasive carcinoma [BRCA], colon adenocarcinoma [COAD], and glioblastoma [GBM]) mixed with those four immune cell mixtures separately, input titrations of cell-free (cf) DNA from one plasma sample and DNA from formalin-fixed paraffin-embedded (FFPE) tissues, cfDNA from 106 cerebrospinal fluids (CSF) and 42 other body fluids, and DNA from 37 FFPE tissues.

We sequenced all the samples mentioned above using FLEXseq. Paired-end reads were quality and length trimmed with cutadapt version 3.5, and all high-quality sequencing reads were then aligned to the hg38 reference genome using Bismark v0.23.0. We then filtered out reads with unmethylated cytosine in the non-CpG context with filter_non_conversion function. Next, we used the bismark_methylation_extractor function to extract the methylation calls (removing single-nucleotide polymorphisms [SNP]).

We also used the bam2pat function from wgbs_tools, to convert bam files into .pat files for deconvolution, keeping reads covering at least three CpG sites. The .pat files preserve fragment-level data and were de-identified by removing SNPs using the mask_pat function. 

We used CNVkit (v0.9.10) to analyze and visualize genome-wide copy numbers. Our inputs into CNVkit were Bismark/Bowtie 2 aligned BAM files deduplicated by Bismark based on end positions and fragment lengths. We then generated log2copy ratio plots for all body fluid and FFPE samples based on the pooled reference and visualized them across all bins using the DNAcopy R package.
DOI: 10.5281/zenodo.15627769
title: Data for methylome sequencing: Enriching and Profiling Methylomes for Tumor Classification and Liquid Biopsies

description: We benchmarked and demonstrated the versatility of FLEXseq (Fragment Ligation EXclusive methylation sequencing) across different sample types: genomic DNA from the K562 (leukemia) cell line, DNA mix-in titrations of four immune cell types (B cells, T cells, monocytes, and neutrophils), DNA titrations of three cancer cell lines (breast invasive carcinoma [BRCA], colon adenocarcinoma [COAD], and glioblastoma [GBM]) mixed with those four immune cell mixtures separately, input titrations of cell-free (cf) DNA from one plasma sample and DNA from formalin-fixed paraffin-embedded (FFPE) tissues, cfDNA from 106 cerebrospinal fluids (CSF) and 42 other body fluids, and DNA from 37 FFPE tissues.

We sequenced all the samples mentioned above using FLEXseq. Paired-end reads were quality and length trimmed with cutadapt version 3.5, and all high-quality sequencing reads were then aligned to the hg38 reference genome using Bismark v0.23.0. We then filtered out reads with unmethylated cytosine in the non-CpG context with filter_non_conversion function. Next, we used the bismark_methylation_extractor function to extract the methylation calls (removing single-nucleotide polymorphisms [SNP]).

We also used the bam2pat function from wgbs_tools, to convert bam files into .pat files for deconvolution, keeping reads covering at least three CpG sites. The .pat files preserve fragment-level data and were de-identified by removing SNPs using the mask_pat function. 

We used CNVkit (v0.9.10) to analyze and visualize genome-wide copy numbers. Our inputs into CNVkit were Bismark/Bowtie 2 aligned BAM files deduplicated by Bismark based on end positions and fragment lengths. We then generated log2copy ratio plots for all body fluid and FFPE samples based on the pooled reference and visualized them across all bins using the DNAcopy R package.
DOI: 10.15468/dl.bppfdw
title: Occurrence Download

description: A dataset containing 143300 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is ESA - Herbário da Escola Superior de Agricultura Luiz de Queiroz"
 ]
}

 The dataset includes 143300 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029243-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vzmrm
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epidendrum lanceolatum Bradford ex Griseb."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194710-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xquurp
title: Occurrence Download

description: A dataset containing 1066 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gambelia sila (Stejneger, 1890)"
 ]
}

 The dataset includes 1066 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000799-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w2jvrl
title: Occurrence Download

description: A dataset containing 2352 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Musa ×paradisiaca L."
 ]
}

 The dataset includes 2352 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019730-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5kr7a8
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calibanus hookeri (Lem.) Trel."
 ]
}

 The dataset includes 86 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000799-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j4ucka
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "GadmGid is COL.15.89_2",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 25 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194709-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rmbkqe
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myrcia pinetorum (Britton & P.Wilson) Z.Acosta & K.Samra"
 ]
}

 The dataset includes 16 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0179965-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygcqaw
title: Occurrence Download

description: A dataset containing 739 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myrciaria dubia (Kunth) Mc Vaugh"
 ]
}

 The dataset includes 739 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019743-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cc2rrk
title: Occurrence Download

description: A dataset containing 747102 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Toxostoma rufum Linnaeus, 1758"
 ]
}

 The dataset includes 747102 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000799-171025204727650/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhe3g4
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Viet Nam",
 "OccurrenceStatus is Present",
 "TaxonKey is Emberiza aureola Pallas, 1773"
 ]
}

 The dataset includes 43 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073128-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u5ytt6
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epidendrum lagotis Rchb.f."
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194706-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mmm0s5
title: Occurrence Download

description: A dataset containing 624 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Nicaragua",
 "Country is Costa Rica",
 "Country is Honduras"
 ]
 },
 "Issue is Geodetic datum assumed WGS84",
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Jacaranda mimosifolia D.Don",
 "TaxonKey is Swietenia macrophylla G.King",
 "TaxonKey is Swietenia humilis Zucc.",
 "TaxonKey is Carapa guianensis Aubl.",
 "TaxonKey is Cedrela odorata L.",
 "TaxonKey is Dalbergia retusa Hemsl."
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 624 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000799-171109162308116/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qb5hv
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palicourea tsakiana (C.M.Taylor) C.M.Taylor"
 ]
}

 The dataset includes 96 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0179964-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ebnujr
title: Occurrence Download

description: A dataset containing 8672 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Mexico",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "TaxonKey is Aspidoscelis gularis (Baird & Girard, 1852)"
 ]
}

 The dataset includes 8672 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194712-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.