cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.rdb74s
title: Occurrence Download

description: A dataset containing 40631 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Caprimulgus affinis Horsfield, 1821)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40631 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0292767-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jwmza5
title: Occurrence Download

description: A dataset containing 15085 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vulpes lagopus (Linnaeus, 1758)"
 ]
}

 The dataset includes 15085 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139194-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fb6rh6
title: Occurrence Download

description: A dataset containing 12443 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Casuarina cunninghamiana Miq.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 12443 records from 162 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006344-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r39r68
title: Occurrence Download

description: A dataset containing 12678 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Pseudotriton ruber (Sonnini de Manoncourt & Latreille, 1801))"
 ]
}

 The dataset includes 12678 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003817-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14710071
title: Datasets for SVR-PK screening
DOI: 10.5281/zenodo.14710072
title: Datasets for SVR-PK screening
DOI: 10.15468/dl.xg8yj3
title: Occurrence Download

description: A dataset containing 987 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Atelopus spurrelli Boulenger, 1914"
 ]
}

 The dataset includes 987 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000736-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10570448
title: The North Pacific Eukaryotic Gene Catalog: clustered nucleotide metatranscripts and read counts

description: This data continues with the development of the NPEGC Trinity de novo metatranscriptome assemblies from the protein data repository of The North Pacific Eukaryotic Gene Catalog. The nucleotide sequences corresponding to the NPEGC cluster representatives are collected together in these repository files:NPac.G1PA.bf100.id99.nt.fasta.gzNPac.G2PA.bf100.id99.nt.fasta.gzNPac.G3PA.bf100.id99.nt.fasta.gzNPac.G3PA_diel.bf100.id99.nt.fasta.gzNPac.D1PA.bf100.id99.nt.fasta.gzA full description of this data is published in Scientific Data, available here: The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Please cite this publication if your research uses this data:Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161.These nucleotide sequences have been sourced from the Zenodo repository for raw assemblies: The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3

Key processing steps are sampled below with links to the detailed code on the main github code repository: https://github.com/armbrustlab/NPac_euk_gene_catalog

Code used to build the kallisto indices and map the short reads against indices with kallisto are online in the code repository here: NPEGC.nt_kallisto_counts.shThere are two main steps:1. Generate the kallisto index on the sets of clustered nucleotide metatranscripts2. Map the short reads from environmental samples back to the assembly index

As generated above, kallisto generates separate results files for each of the sample files. Even after compression, the total size of the tarballed kallisto output results directories are prohibitively large (>50GB). We use the code in this template R script to join together the 'est_count' estimated count values for the tens of millions of protein sequences in each project metatranscriptome, along with length.

The code in this template script was used for each project: aggregate_kallisto_counts.RThe output count files for each project are Gzip-compressed and uploaded to the NPEGC nucleotide data repository here: 

G1PA.raw.est_counts.csv.gzG2PA.raw.est_counts.csv.gzG3PA.raw.est_counts.csv.gzG3PA_diel.raw.est_counts.csv.gzD1PA.raw.est_counts.csv.gz
DOI: 10.5281/zenodo.10570449
title: The North Pacific Eukaryotic Gene Catalog: clustered nucleotide metatranscripts and read counts

description: This data continues with the development of the NPEGC Trinity de novo metatranscriptome assemblies from the protein data repository of The North Pacific Eukaryotic Gene Catalog. The nucleotide sequences corresponding to the NPEGC cluster representatives are collected together in these repository files:NPac.G1PA.bf100.id99.nt.fasta.gzNPac.G2PA.bf100.id99.nt.fasta.gzNPac.G3PA.bf100.id99.nt.fasta.gzNPac.G3PA_diel.bf100.id99.nt.fasta.gzNPac.D1PA.bf100.id99.nt.fasta.gzThese nucleotide sequences have been sourced from the Zenodo repository for raw assemblies: The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3

Key processing steps are sampled below with links to the detailed code on the main github code repository: https://github.com/armbrustlab/NPac_euk_gene_catalog

Code used to build the kallisto indices and map the short reads against indices with kallisto are online in the code repository here: NPEGC.nt_kallisto_counts.shThere are two main steps:1. Generate the kallisto index on the sets of clustered nucleotide metatranscripts2. Map the short reads from environmental samples back to the assembly index

As generated above, kallisto generates separate results files for each of the sample files. Even after compression, the total size of the tarballed kallisto output results directories are prohibitively large (>50GB). We use the code in this template R script to join together the 'est_count' estimated count values for the tens of millions of protein sequences in each project metatranscriptome, along with length.

The code in this template script was used for each project: aggregate_kallisto_counts.RThe output count files for each project are Gzip-compressed and uploaded to the NPEGC nucleotide data repository here: 

G1PA.raw.est_counts.csv.gzG2PA.raw.est_counts.csv.gzG3PA.raw.est_counts.csv.gzG3PA_diel.raw.est_counts.csv.gzD1PA.raw.est_counts.csv.gz
DOI: 10.5281/zenodo.13826820
title: The North Pacific Eukaryotic Gene Catalog: clustered nucleotide metatranscripts and read counts

description: This data continues with the development of the NPEGC Trinity de novo metatranscriptome assemblies from the protein data repository of The North Pacific Eukaryotic Gene Catalog. The nucleotide sequences corresponding to the NPEGC cluster representatives are collected together in these repository files:NPac.G1PA.bf100.id99.nt.fasta.gzNPac.G2PA.bf100.id99.nt.fasta.gzNPac.G3PA.bf100.id99.nt.fasta.gzNPac.G3PA_diel.bf100.id99.nt.fasta.gzNPac.D1PA.bf100.id99.nt.fasta.gzA full description of this data is published in Scientific Data, available here: The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Please cite this publication if your research uses this data:Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161.These nucleotide sequences have been sourced from the Zenodo repository for raw assemblies: The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3

Key processing steps are sampled below with links to the detailed code on the main github code repository: https://github.com/armbrustlab/NPac_euk_gene_catalog

Code used to build the kallisto indices and map the short reads against indices with kallisto are online in the code repository here: NPEGC.nt_kallisto_counts.shThere are two main steps:1. Generate the kallisto index on the sets of clustered nucleotide metatranscripts2. Map the short reads from environmental samples back to the assembly index

As generated above, kallisto generates separate results files for each of the sample files. Even after compression, the total size of the tarballed kallisto output results directories are prohibitively large (>50GB). We use the code in this template R script to join together the 'est_count' estimated count values for the tens of millions of protein sequences in each project metatranscriptome, along with length.

The code in this template script was used for each project: aggregate_kallisto_counts.RThe output count files for each project are Gzip-compressed and uploaded to the NPEGC nucleotide data repository here: 

G1PA.raw.est_counts.csv.gzG2PA.raw.est_counts.csv.gzG3PA.raw.est_counts.csv.gzG3PA_diel.raw.est_counts.csv.gzD1PA.raw.est_counts.csv.gz
DOI: 10.15468/dl.cqw5vu
title: Occurrence Download

description: A dataset containing 5155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Silene armeria L."
 ]
}

 The dataset includes 5155 records from 240 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000737-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13743266
title: The North Pacific Eukaryotic Gene Catalog: KOfam protein function annotations

description: KEGG functional annotation using KofamScan v1.3.0

These tables are larger alternative versions to the KOfam tables included in the North Pacific Eukaryotic Gene Catalog protein data repository here: https://zenodo.org/records/12630398A full description of this data is published in Scientific Data, available here: The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Please cite this publication if your research uses this data:Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161.Clustered protein sequences were annotated against the KEGG collection (release 104.0) of 20,819 protein family Hidden Markov Models (HMMs) using KofamScan and KofamKOALA. Kofam annotation code is documented in the project github repository here: NPEGC.kofamscan_function.sh

Excerpt of core NPEGC_kofam function:

# Define input FASTAlocal INPUT_FASTA="NPac.${STUDY}.bf100.id99.aa.fasta"

# KofamScan call${KOFAM_DIR}/kofam_scan-1.3.0/exec_annotation -f detail-tsv -E ${EVALUE} -o ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.tsv ${FASTA_DIR}/${INPUT_FASTA}

Unprocessed annotation results were filtered with a minimum score of 30 to remove low-scoring matches:zcat NPac.NPacID.kofam.tsv.gz | awk -F'\t' '{ gsub(/"/, "", $5); $5 = $5 + 0; if ($5 >= 30) print }' | gzip > NPac.NPacID.UW.bf100.id99.aa.incT30.tsv.gz
DOI: 10.5281/zenodo.13743267
title: The North Pacific Eukaryotic Gene Catalog: KOfam protein function annotations

description: KEGG functional annotation using KofamScan v1.3.0

These tables are larger alternative versions to the KOfam tables included in the North Pacific Eukaryotic Gene Catalog protein data repository here: https://zenodo.org/records/12630398A full description of this data is published in Scientific Data, available here: The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Please cite this publication if your research uses this data:Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161.Clustered protein sequences were annotated against the KEGG collection (release 104.0) of 20,819 protein family Hidden Markov Models (HMMs) using KofamScan and KofamKOALA. Kofam annotation code is documented in the project github repository here: NPEGC.kofamscan_function.sh

Excerpt of core NPEGC_kofam function:

# Define input FASTAlocal INPUT_FASTA="NPac.${STUDY}.bf100.id99.aa.fasta"

# KofamScan call${KOFAM_DIR}/kofam_scan-1.3.0/exec_annotation -f detail-tsv -E ${EVALUE} -o ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.tsv ${FASTA_DIR}/${INPUT_FASTA}

Unprocessed annotation results were filtered with a minimum score of 30 to remove low-scoring matches:zcat NPac.NPacID.kofam.tsv.gz | awk -F'\t' '{ gsub(/"/, "", $5); $5 = $5 + 0; if ($5 >= 30) print }' | gzip > NPac.NPacID.UW.bf100.id99.aa.incT30.tsv.gz
DOI: 10.5281/zenodo.7055912
title: MarFERReT: an open-source, version-controlled reference library of marine microbial eukaryote functional genes

description: The emerging field of environmental metatranscriptomics generates large volumes of sequence data about actively transcribed genes in natural environments, and taxonomic annotation of these sequences are dependent on curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data and approximately half of eukaryotic environmental transcripts can be annotated. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), an updated marine microbial eukaryotic sequence library with version-controlled contents designed for taxonomic annotation of eukaryotic metatranscriptomes. MarFERReT contains over 30 million protein sequences from 899 marine eukaryotic genomes and transcriptomes, covering 503 species and 323 genera. Continued expansion of MarFERReT as new reference sequences become available will enable up-to-date taxonomic annotations into the future.<br> <br> Please see the MarFERReT GitHub repository for full code, documentation and updates:<br> https://github.com/armbrustlab/marferret
DOI: 10.15468/dl.6wdxyv
title: Occurrence Download

description: A dataset containing 841454 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-79.18355 0.75802,-79.22424 0.43252,-79.22424 0.15786,-78.9801 0.08665,-78.17647 -0.01507,-78.11544 0.57493,-78.32906 0.63596,-78.60372 0.71733,-79.18355 0.75802))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2010-2025"
 ]
}

 The dataset includes 841454 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000733-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14352714
title: Data for "Probing the fluctuating magnetic field of Fe-triazole spin-crossover thin-layers with nitrogen-vacancy centers in diamond"

description: In this Zenodo repository, the data as plotted in "Probing the fluctuating magnetic field of Fe-triazole spin-crossover thin-layers with nitrogen-vacancy centers in diamond" is uploaded. The file consists of folders named after the figures in the manuscript, where each folder contains csv files and a readme file in which additional information can be found. If a fit function is plotted in a figure, the fit data is also given in a csv file.
DOI: 10.5281/zenodo.14352715
title: Data for "Probing the fluctuating magnetic field of Fe-triazole spin-crossover thin-layers with nitrogen-vacancy centers in diamond"

description: In this Zenodo repository, the data as plotted in "Probing the fluctuating magnetic field of Fe-triazole spin-crossover thin-layers with nitrogen-vacancy centers in diamond" is uploaded. The file consists of folders named after the figures in the manuscript, where each folder contains csv files and a readme file in which additional information can be found. If a fit function is plotted in a figure, the fit data is also given in a csv file.
DOI: 10.5281/zenodo.14715400
title: Data for "Probing the fluctuating magnetic field of Fe-triazole spin-crossover thin-layers with nitrogen-vacancy centers in diamond"

description: In this Zenodo repository, the data as plotted in "Probing the fluctuating magnetic field of Fe-triazole spin-crossover thin-layers with nitrogen-vacancy centers in diamond" is uploaded. The file consists of folders named after the figures in the manuscript, where each folder contains csv files and a readme file in which additional information can be found. If a fit function is plotted in a figure, the fit data is also given in a csv file.
DOI: 10.15468/dl.6e4mhq
title: Occurrence Download

description: A dataset containing 13623 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-79.05962 0.29369,-79.19437 -0.09545,-79.13779 -0.35893,-78.83537 -0.41619,-78.45283 -0.24847,-78.3881 0.08404,-78.71472 0.36947,-79.05962 0.29369))",
 "HasGeospatialIssue is false",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 13623 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000739-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pfahrn
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Philippines",
 "TaxonKey is Gallicolumba keayi (W.E.Clarke, 1900)"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000740-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97g3us
title: Occurrence Download

description: A dataset containing 1055 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Philippines",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ceyx cyanopectus Lafresnaye, 1840"
 ]
}

 The dataset includes 1055 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000741-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j37y5k
title: Occurrence Download

description: A dataset containing 372 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acraea issoria Hübner, 1816"
 ]
}

 The dataset includes 372 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000743-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25959/749g-1h46
title: Havre Volcano RR1506 Voyage Report

description: This is the voyage report for RR1506 voyage to Havre volcano in 2015. Citation: Soule, S., and Carey, R. 2015. Mapping, Exploration and Sampling at Havre Volcano. RR1506. Voyage Report.
DOI: 10.6084/m9.figshare.28251656.v1
title: Summary statistics from trajectory GWAS using repeated eGFR measurements

description: GWAS of eGFR Using Repeated Measurements: Insights from a Longitudinal Analysis<br>
DOI: 10.15468/dl.pcghtv
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tetrao urogalloides Middendorff, 1853"
 ]
}

 The dataset includes 99 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000746-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28251656
title: Genome-Wide Association Study of eGFR Using Repeated Measurements: Insights from a Longitudinal Analysis

description: GWAS of eGFR Using Repeated Measurements: Insights from a Longitudinal Analysis<br>
DOI: 10.6084/m9.figshare.28251656.v2
title: Summary statistics from trajectory GWAS using repeated eGFR measurements

description: GWAS of eGFR Using Repeated Measurements: Insights from a Longitudinal Analysis<br>
DOI: 10.6084/m9.figshare.28251656.v3
title: Genome-Wide Association Study of eGFR Using Repeated Measurements: Insights from a Longitudinal Analysis

description: GWAS of eGFR Using Repeated Measurements: Insights from a Longitudinal Analysis<br>
DOI: 10.5281/zenodo.14715420
title: predict
DOI: 10.5281/zenodo.14715421
title: predict
DOI: 10.5281/zenodo.14715411
title: Bibliographic Database on Publications about Cannabis sativa (1974–2024)

description: This bibliographic database compiles publications related to Cannabis sativa published between 1974 and 2024. It includes key information on scientific research, such as titles, authors, publication years, keywords, abstracts, and sources. The database is designed to facilitate bibliometric analysis, identify research trends, and explore emerging areas related to Cannabis sativa.
DOI: 10.5281/zenodo.14715412
title: Bibliographic Database on Publications about Cannabis sativa (1974–2024)

description: This bibliographic database compiles publications related to Cannabis sativa published between 1974 and 2024. It includes key information on scientific research, such as titles, authors, publication years, keywords, abstracts, and sources. The database is designed to facilitate bibliometric analysis, identify research trends, and explore emerging areas related to Cannabis sativa.
DOI: 10.25582/data.2020-03.1959115/2364489
title: Data for EMSL Project 49229 from March 2020
DOI: 10.25582/data.2020-03.1965673/2364490
title: Data for EMSL Project 49229 from March 2020
DOI: 10.15468/dl.627v9g
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Galium flavescens Borbás ex Simonk.",
 "HasCoordinate is true",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019705-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.