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

description: A dataset containing 25315 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Euodia J.R.Forst. & G.Forst.",
 "TaxonKey is Halfordia F.Muell.",
 "TaxonKey is Melicope J.R.Forst. & G.Forst."
 ]
}

 The dataset includes 25315 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009353-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hn5tkg
title: Occurrence Download

description: A dataset containing 110 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 Calyptorhynchus baudinii Lear, 1832"
 ]
}

 The dataset includes 110 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055263-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mjm4ck
title: Occurrence Download

description: A dataset containing 1935926 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "Geometry POLYGON ((138.0456 -35.34896, 138.8481 -35.34896, 138.8481 -34.61298, 138.0456 -34.61298, 138.0456 -35.34896))"
 ]
}

 The dataset includes 1935926 records from 364 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047782-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x8molg
title: Occurrence Download

description: A dataset containing 295 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pyrus syriaca Boiss.",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1970",
 "Year is less than or equal to 2017",
 "DecimalLongitude is greater than or equal to -15",
 "DecimalLongitude is less than or equal to 40",
 "DecimalLatitude is greater than or equal to 30",
 "DecimalLatitude is less than or equal to 75"
 ]
}

 The dataset includes 295 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009353-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hggy2u
title: Occurrence Download

description: A dataset containing 438 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 Cacatua leadbeateri (Vigors, 1831)"
 ]
}

 The dataset includes 438 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055268-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aawcrx
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Specimen)",
 "Country is French Guiana",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Morphnus guianensis (Daudin, 1800)"
 ]
}

 The dataset includes 32 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047785-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gy2w1g
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limonium dodartii (Girard) Kuntze",
 "DatasetKey is CSIC-Real Jardín Botánico-Anthos. Sistema de Información de las Plantas de España"
 ]
}

 The dataset includes 16 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009354-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vpjv5a
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Begonia medogensis Jian W.Li, Y.H.Tan & X.H.Jin"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055291-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b2hthz
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eremurus zenaidae Vved."
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047793-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6iss8s
title: Occurrence Download

description: A dataset containing 200 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Arthroleptis variabilis Matschie, 1893",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 200 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010532-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hgerna
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bulbophyllum crocodilus J.J.Sm."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074061-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3auuw5
title: Occurrence Download

description: A dataset containing 152029 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mercurialis annua L."
 ]
}

 The dataset includes 152029 records from 1159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074105-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11238290
title: RNAseq of Mus musculus lung tissue
title: NF-CORE/rnaseq pipeline outputs

description: RNAseq was performed on mouse lung tissue samples to assess the effects of antibiotic treatment on airway gene transcriptional programs. The effect of antibiotics treatment was primarily investigated in conjunction with the age of treatment onset, with some mice starting treatment at 3-weeks of old (young) while others started at 8-weeks old (old). Secondly, comparisons were made following cohousing of the mice (to normalise the gut microbiome) following their course of antibiotics. These experiments are referred to as "Abx-treated" and "Cohoused" in the accompanying metadata file.

The RNA sequencing raw fastq files have been processed using the NF-CORE rnaseq pipeline. Briefly, reads undergo initial QC with FastQC, UMIs are extracted with UMI-tools, and reads undergo adapter removal and quality trimming using Trim Galore! Next, genomic contaminants are removed via BBSplit, and ribosomal components are removed via SortMeRNA. Reads are aligned and quantified via a combination of STAR and Salmon tools, and sorted and indexed using SAMtools and dereplicated via UMI-tools. Outputs are provided in .rds file format as SummarizedExperiment objects, with bias-corrected gene counts without an offset (perdijk_abx_study_2024_RNA.gene_counts_length_scaled.rds). A .csv file of the corrected counts table has also been provided (perdijk_abx_study_2024_RNA.gene_counts_length_scaled.csv).

There are two matrices provided in the .rds file: counts and abundance.



The abundance matrix is the scaled and normalised transcripts per million (TPM) abundance. TPM explicitly erases information about library size. That is, it estimates the relative abundance of each transcript proportional to the total population of transcripts sampled in the experiment. Thus, you can imagine TPM, in a way, as a partition of unity — we want to assign a fraction of the total expression (whatever that may be) to transcript, regardless of whether our library is 10M fragments or 100M fragments.

The counts matrix is a re-estimated counts table that aims to provide count-level data to be compatible with downstream tools such as DESeq2.

The tximport package has a single function for importing transcript-level estimates. The type argument is used to specify what software was used for estimation. A simple list with matrices, "abundance", "counts", and "length", is returned, where the transcript level information is summarized to the gene-level. Typically, abundance is provided by the quantification tools as TPM (transcripts-per-million), while the counts are estimated counts (possibly fractional), and the "length" matrix contains the effective gene lengths. The "length" matrix can be used to generate an offset matrix for downstream gene-level differential analysis of count matrices.
DOI: 10.5281/zenodo.11238291
title: RNAseq of Mus musculus lung tissue
title: NF-CORE/rnaseq pipeline outputs

description: RNAseq was performed on mouse lung tissue samples to assess the effects of antibiotic treatment on airway gene transcriptional programs. The effect of antibiotics treatment was primarily investigated in conjunction with the age of treatment onset, with some mice starting treatment at 3-weeks of old (young) while others started at 8-weeks old (old). Secondly, comparisons were made following cohousing of the mice (to normalise the gut microbiome) following their course of antibiotics. These experiments are referred to as "Abx-treated" and "Cohoused" in the accompanying metadata file.

The RNA sequencing raw fastq files have been processed using the NF-CORE rnaseq pipeline. Briefly, reads undergo initial QC with FastQC, UMIs are extracted with UMI-tools, and reads undergo adapter removal and quality trimming using Trim Galore! Next, genomic contaminants are removed via BBSplit, and ribosomal components are removed via SortMeRNA. Reads are aligned and quantified via a combination of STAR and Salmon tools, and sorted and indexed using SAMtools and dereplicated via UMI-tools. Outputs are provided in .rds file format as SummarizedExperiment objects, with bias-corrected gene counts without an offset (perdijk_abx_study_2024_RNA.gene_counts_length_scaled.rds). A .csv file of the corrected counts table has also been provided (perdijk_abx_study_2024_RNA.gene_counts_length_scaled.csv).

There are two matrices provided in the .rds file: counts and abundance.



The abundance matrix is the scaled and normalised transcripts per million (TPM) abundance. TPM explicitly erases information about library size. That is, it estimates the relative abundance of each transcript proportional to the total population of transcripts sampled in the experiment. Thus, you can imagine TPM, in a way, as a partition of unity — we want to assign a fraction of the total expression (whatever that may be) to transcript, regardless of whether our library is 10M fragments or 100M fragments.

The counts matrix is a re-estimated counts table that aims to provide count-level data to be compatible with downstream tools such as DESeq2.

The tximport package has a single function for importing transcript-level estimates. The type argument is used to specify what software was used for estimation. A simple list with matrices, "abundance", "counts", and "length", is returned, where the transcript level information is summarized to the gene-level. Typically, abundance is provided by the quantification tools as TPM (transcripts-per-million), while the counts are estimated counts (possibly fractional), and the "length" matrix contains the effective gene lengths. The "length" matrix can be used to generate an offset matrix for downstream gene-level differential analysis of count matrices.
DOI: 10.15468/dl.447p5c
title: Occurrence Download

description: A dataset containing 410 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saurida macrolepis Tanaka, 1917",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 410 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001190-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbujgx
title: Occurrence Download

description: A dataset containing 860885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Andrena Fabricius, 1775",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 860885 records from 962 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001182-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10637078
title: Appendix to "Evaluating Interactive Documentation for Programmers"

description: This appendix supplements our manuscript "Evaluating Interactive Documentation for Programmers", currently under revision.
DOI: 10.5281/zenodo.10637079
title: Appendix to "Evaluating Interactive Documentation for Programmers"

description: This appendix supplements our manuscript "Evaluating Interactive Documentation for Programmers", currently under revision.
DOI: 10.5281/zenodo.14868205
title: Appendix to "Evaluating Interactive Documentation for Programmers"

description: This appendix supplements our manuscript "Evaluating Interactive Documentation for Programmers", currently under revision.
DOI: 10.15468/dl.8eb544
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saurida tweddlei Russell, 2015",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001191-250213122211068/datasets/export for details.
DOI: 10.5281/zenodo.13309431
title: Effect of Drying Methods on the Properties of Ginger Powder and Its Application in Gummy Candy Production
title: Impact of Pretreatment on Ginger Powder Characteristics

description: The data provides the parameters of the research process, with specific contents in the following sheets:

The "Approximate Composition" sheet provides information on the basic composition of raw ginger.

The "Color" sheet provides the color value of ginger powder.

The "Physical" sheet provides the physical characteristics of ginger powder, such as bulk density, tap density, flowability, compressibility, solubility, hygroscopicity, and particle size.

The "Biological Compounds" sheet provides information on the content of active ingredients such as total polyphenol, total flavonoid, gingerol, alkaloids, and tannins.

The "Antioxidant Activity" sheet provides information on the antioxidant capacity of ginger powder with antioxidant values through DPPH and ABTS free radical scavenging ability and FRAP iron reducing ability.

The "PCA" sheet shows the data obtained while performing principal component analysis.

The "Pearson" sheet shows the data obtained during the Pearson correlation evaluation.

The sheets with the names physical of ginger gummy candy, texture profile, and sensory evaluation show the results related to the properties of the ginger gummy candies.

The data is currently available only to authors, editors, and reviewers and will be made public once the manuscript is accepted.
DOI: 10.5281/zenodo.14773290
title: Effect of Drying Methods on the Properties of Ginger Powder and Its Application in Gummy Candy Production
title: Impact of Pretreatment on Ginger Powder Characteristics

description: The data provides the parameters of the research process, with specific contents in the following sheets:

The "Approximate Composition" sheet provides information on the basic composition of raw ginger.

The "Color" sheet provides the color value of ginger powder.

The "Physical" sheet provides the physical characteristics of ginger powder, such as bulk density, tap density, flowability, compressibility, solubility, hygroscopicity, and particle size.

The "Biological Compounds" sheet provides information on the content of active ingredients such as total polyphenol, total flavonoid, gingerol, alkaloids, and tannins.

The "Antioxidant Activity" sheet provides information on the antioxidant capacity of ginger powder with antioxidant values through DPPH and ABTS free radical scavenging ability and FRAP iron reducing ability.

The "PCA" sheet shows the data obtained while performing principal component analysis.

The "Pearson" sheet shows the data obtained during the Pearson correlation evaluation.

The sheets with the names physical of ginger gummy candy, texture profile, and sensory evaluation show the results related to the properties of the ginger gummy candies.

The data is currently available only to authors, editors, and reviewers and will be made public once the manuscript is accepted.
DOI: 10.5281/zenodo.14864799
title: UnionH: A Multi-Cohort Gastric Cancer Dataset for Transcriptomics and Proteomics Analysis

description: This dataset includes three clinical cohorts of gastric cancer (GC) patients from Fujian Medical University Union Hospital and Zhangzhou Affiliated Hospital. 

The UnionH-1 cohort (50 NACI-treated GC patients) is used for bulk gene expression profiling.

The UnionH-2 cohort (9 treatment-naïve GC patients) is employed for spatial transcriptome analysis.

The UnionH-3 cohort (10 GC patients) includes gastroscopy samples analyzed via IMC. Patient data include clinicopathological features, TNM staging, and follow-up information.
DOI: 10.15468/dl.99y8hv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Squalus vulipinis (Bonnaterre, 1788)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001192-250213122211068/datasets/export for details.
DOI: 10.5281/zenodo.14868221
title: CAUSES OF ATOPIC DERMATITIS AND MEASURES FOR ITS PREVENTION
DOI: 10.5281/zenodo.14868222
title: CAUSES OF ATOPIC DERMATITIS AND MEASURES FOR ITS PREVENTION
DOI: 10.15468/dl.3m6j3v
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kajikia audax (Philippi, 1887)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001193-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14868226
title: NEW-GENERATION COMPOSITE MATERIALS: ADVANCES IN MANUFACTURING TECHNOLOGY
DOI: 10.5281/zenodo.14868227
title: NEW-GENERATION COMPOSITE MATERIALS: ADVANCES IN MANUFACTURING TECHNOLOGY
DOI: 10.15468/dl.bgcvus
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pleuronectes herzensteini (Jordan & Snyder, 1901)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001194-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.du6z4n
title: Occurrence Download

description: A dataset containing 233 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Testudines)",
 "StateProvince is one of (arauca)"
 ]
 }
 ]
}

 The dataset includes 233 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001195-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwx29z
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limanda herzensteini Jordan & Snyder, 1901",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001196-250213122211068/datasets/export for details.
DOI: 10.15468/dl.d7jugf
title: Occurrence Download

description: A dataset containing 1382 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Testudines)",
 "StateProvince is one of (vichada)"
 ]
 }
 ]
}

 The dataset includes 1382 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001197-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gczzsq
title: Occurrence Download

description: A dataset containing 321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudopleuronectes yokohamae (Günther, 1877)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 321 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001199-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vvcx8m
title: Occurrence Download

description: A dataset containing 8981 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 8981 records from 282 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001200-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.