cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6412150
title: Global extinction probabilities of terrestrial, freshwater, and marine species groups

description: This is the dataset presented in the manuscript titled "Global extinction probabilities of terrestrial, freshwater, and marine species groups". The dataset gives the code (R code), as well as the resulting raster files for the suggested Global extinction probabilities for different taxonomic groups, for use in Life Cycle Impact Assessment (LCIA). We supply the results on 5arc minute resolution, aggregated for relevant spatial scales (e.g. terrestrial ecoregions or watersheds), as well as at country scale. For application in LCIA, we recommend applying GEPs to CFs with corresponding species groups and spatial scales. If the species group of the CFs do not match any of the provided GEPs, see (1); if the spatial scale of the CFs do not match any of the provided GEPs, see (2). If the species groups of the CFs do not match any of the provided sets of GEPs, we recommend recalculating GEPs for corresponding species groups and spatial scales based on the provided R scripts (e.g., see the R script for the freshwater heterotroph GEPs). Alternatively, GEPs can be aggregated to species group combinations by calculating species number-weighted GEP averages of the existing GEPs (see Table 4 in the article for species numbers per species group). In case of the latter approach, we recommend calculate GEP averages for all regions across the world (and not just those included in the analysis) and normalise the region-level average GEPs by the sum of the region-level average GEPs for consistency with the GEP concept. In addition to species group aggregation, GEPs can be aggregated to different spatial scales by calculating the sum of the cell-level GEPs contained per region (e.g., see R scripts).
DOI: 10.5281/zenodo.7462157
title: Global extinction probabilities of terrestrial, freshwater, and marine species groups

description: This is the dataset presented in the manuscript titled "Global extinction probabilities of terrestrial, freshwater, and marine species groups". The dataset gives the code (R code), as well as the resulting raster files for the suggested Global extinction probabilities for different taxonomic groups, for use in Life Cycle Impact Assessment (LCIA). We supply the results on 5arc minute resolution, aggregated for relevant spatial scales (e.g. terrestrial ecoregions or watersheds), as well as at country scale. For application in LCIA, we recommend applying GEPs to CFs with corresponding species groups and spatial scales. If the species group of the CFs do not match any of the provided GEPs, see (1); if the spatial scale of the CFs do not match any of the provided GEPs, see (2). If the species groups of the CFs do not match any of the provided sets of GEPs, we recommend recalculating GEPs for corresponding species groups and spatial scales based on the provided R scripts (e.g., see the R script for the freshwater heterotroph GEPs). Alternatively, GEPs can be aggregated to species group combinations by calculating species number-weighted GEP averages of the existing GEPs (see Table 4 in the article for species numbers per species group). In case of the latter approach, we recommend calculate GEP averages for all regions across the world (and not just those included in the analysis) and normalise the region-level average GEPs by the sum of the region-level average GEPs for consistency with the GEP concept. In addition to species group aggregation, GEPs can be aggregated to different spatial scales by calculating the sum of the cell-level GEPs contained per region (e.g., see R scripts).
DOI: 10.6084/m9.figshare.c.3630299_d9.v1
title: Additional file 6: of Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs

description: The list of differentially methylated genes. (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.c.3630299_d6.v1
title: Additional file 11: of Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs

description: The genes identified by signal-net analysis. (XLS 51Â kb)
DOI: 10.6084/m9.figshare.c.3630317_d1.v1
title: Additional file 1: Table S1. of Gene name errors are widespread in the scientific literature

description: List of supplementary files containing Excel gene name errors from journals and Gene Expression Omnibus (GEO). (XLSX 81 kb)
DOI: 10.6084/m9.figshare.c.3630299_d4.v1
title: Additional file 9: of Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs

description: Significant pathways related with up-methylated genes and the genes involved. (XLSX 81Â kb)
DOI: 10.6084/m9.figshare.c.3630299_d1.v1
title: Additional file 10: of Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs

description: Significant pathways related with down-methylated genes and the genes involved. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3630254_d4.v1
title: Additional file 4: of Complete genome sequence and genomic characterization of Microcystis panniformis FACHB 1757 by third-generation sequencing

description: Annotation of three candidate CRISPR clusters on the chromosome sequence and one CRISPR cluster on the plasmid using strict parameters. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3630254_d2.v1
title: Additional file 2: of Complete genome sequence and genomic characterization of Microcystis panniformis FACHB 1757 by third-generation sequencing

description: The COG function annotation in each COG cluster. (XLSX 114Â kb)
DOI: 10.6084/m9.figshare.c.3630254_d1.v1
title: Additional file 3: of Complete genome sequence and genomic characterization of Microcystis panniformis FACHB 1757 by third-generation sequencing

description: N 4 -methylcytosine, N 6 -methyladenine, and other modified bases throughout the whole chromosome. (XLSX 7893Â kb)
DOI: 10.6084/m9.figshare.c.3630197_d7.v1
title: Additional file 2: Table S2. of Mapping a major QTL responsible for dwarf architecture in Brassica napus using a single-nucleotide polymorphism marker approach

description: Detailed SNP genetic map. (XLSX 296Â kb)
DOI: 10.6084/m9.figshare.c.3630188_d13.v1
title: Additional file 1: of Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality

description: Summary of metatranscriptome processing, assembly and annotation steps. This table provides summary statistics for read processing steps applied to each dataset. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3630197_d6.v1
title: Additional file 6: Table S3. of Mapping a major QTL responsible for dwarf architecture in Brassica napus using a single-nucleotide polymorphism marker approach

description: Genes on the mapped segments of chromosome C05 of Brassica napus. (XLSX 22Â kb)
DOI: 10.5281/zenodo.14499582
title: Global extinction probabilities of terrestrial, freshwater, and marine species groups

description: This is the updated dataset presented in the manuscript titled "Global extinction probabilities of terrestrial, freshwater, and marine species groups".

The dataset gives the code (R code), as well as the resulting raster files for the suggested Global extinction probabilities for different taxonomic groups, for use in Life Cycle Impact Assessment (LCIA). We supply the results on 5arc minute resolution, aggregated for relevant spatial scales (e.g. terrestrial ecoregions or watersheds), as well as at country scale.

For application in LCIA, we recommend applying GEPs to CFs with corresponding species groups and spatial scales. If the species group of the CFs do not match any of the provided GEPs, see (1); if the spatial scale of the CFs do not match any of the provided GEPs, see (2).



If the species groups of the CFs do not match any of the provided sets of GEPs, we recommend recalculating GEPs for corresponding species groups and spatial scales based on the provided R scripts (e.g., see the R script for the freshwater heterotroph GEPs). Alternatively, GEPs can be aggregated to species group combinations by calculating species number-weighted GEP averages of the existing GEPs (see Table 4 in the article for species numbers per species group). In case of the latter approach, we recommend calculate GEP averages for all regions across the world (and not just those included in the analysis) and normalise the region-level average GEPs by the sum of the region-level average GEPs for consistency with the GEP concept.

In addition to species group aggregation, GEPs can be aggregated to different spatial scales by calculating the sum of the cell-level GEPs contained per region (e.g., see R scripts).


 

Updates: corrected mistakes in cnidarians. Removedcpiuntry GEPs for marine species groups.
DOI: 10.5281/zenodo.6412149
title: Global extinction probabilities of terrestrial, freshwater, and marine species groups

description: This is the updated dataset presented in the manuscript titled "Global extinction probabilities of terrestrial, freshwater, and marine species groups".

The dataset gives the code (R code), as well as the resulting raster files for the suggested Global extinction probabilities for different taxonomic groups, for use in Life Cycle Impact Assessment (LCIA). We supply the results on 5arc minute resolution, aggregated for relevant spatial scales (e.g. terrestrial ecoregions or watersheds), as well as at country scale.

For application in LCIA, we recommend applying GEPs to CFs with corresponding species groups and spatial scales. If the species group of the CFs do not match any of the provided GEPs, see (1); if the spatial scale of the CFs do not match any of the provided GEPs, see (2).



If the species groups of the CFs do not match any of the provided sets of GEPs, we recommend recalculating GEPs for corresponding species groups and spatial scales based on the provided R scripts (e.g., see the R script for the freshwater heterotroph GEPs). Alternatively, GEPs can be aggregated to species group combinations by calculating species number-weighted GEP averages of the existing GEPs (see Table 4 in the article for species numbers per species group). In case of the latter approach, we recommend calculate GEP averages for all regions across the world (and not just those included in the analysis) and normalise the region-level average GEPs by the sum of the region-level average GEPs for consistency with the GEP concept.

In addition to species group aggregation, GEPs can be aggregated to different spatial scales by calculating the sum of the cell-level GEPs contained per region (e.g., see R scripts).


 

Updates: corrected mistakes in cnidarians. Removedcpiuntry GEPs for marine species groups.
DOI: 10.15468/dl.cdvtzx
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sepiella japonica Sasaki, 1929",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 13 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036038-241126133413365/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.c.3630110_d1.v1
title: Additional file 1: of The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells

description: Sheet 1: Summery of acquired genomic alterations being selected for during docetaxel exposure in the MCF-7 sub-lines. Sheet 2: Details on the acquired genomic alterations being selected for during docetaxel exposure in the MCF-7 sub-lines. Positions are annotated with Ensembl VEP (version 2.8). The stage (sub-line) in which the alteration was acquired is given along with assigned variant class. Sheet 3: Same as sheet 2, but showing only Class A variation. Sheet 4: Same as sheet 3, but showing only the ‘most severe’ variant per gene. Sheet 5: Summery of acquired genomic alterations being selected for during docetaxel exposure in the MDA-MB-231 sub-lines. Sheet 6: Details on the acquired genomic alterations being selected for during docetaxel exposure in the MDA-MB-231 sub-lines. Positions are annotated with Ensembl VEP (version 2.8). The stage (sub-line) in which the alteration was acquired is given along with assigned variant class. Sheet 7: Same as sheet 6, but showing only Class A variation. Sheet 8: Same as sheet 7, but showing only the ‘most severe’ variant per gene. (XLSX 1113 kb)
DOI: 10.6084/m9.figshare.c.3629969_d3.v1
title: MOESM5 of Epigenetic dynamics of monocyte-to-macrophage differentiation

description: Additional file 5: Table S3. Overview over all identified DMRs and their characteristics.
DOI: 10.6084/m9.figshare.c.3629933_d6.v1
title: MOESM2 of The antioxidative defense system is involved in the premature senescence in transgenic tobacco (Nicotiana tabacum NC89)

description: Additional file 2. Differentially expressed and identified unigenes in photosynthesis, nitrogen metabolism, nutrient reservoir activity, antioxidant activity, ubiquitin-mediated proteolysis, cell growth, and death.
DOI: 10.15468/dl.zmrp3s
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (7fadb370-f921-11dd-af50-b8a03c50a862, c1564d80-1b9d-471c-b84d-8d5dd2efbf0a, 0363cbd4-f666-455e-8e86-0bbddcf51950, 8209258a-80e8-4094-aba2-a3febe5ed45b)",
 "TaxonKey is Pennisetum setaceum (Forssk.) Chiov."
 ]
}

 The dataset includes 95 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036039-241126133413365/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.c.3629942_d3.v1
title: Additional file 2: of Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha

description: Number of 42kD, 22kD and 57kD ORFs included in the pairwise dN/dS analysis. (XLSX 38.5 kb)
DOI: 10.6084/m9.figshare.c.3629933_d3.v1
title: MOESM6 of The antioxidative defense system is involved in the premature senescence in transgenic tobacco (Nicotiana tabacum NC89)

description: Additional file 6. List of primers used for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.c.3629942_d2.v1
title: Additional file 3: of Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha

description: Likelihood comparison of models with dN/dS=1 and dN/dS&lt;1. (XLSX 41.4 kb)
DOI: 10.6084/m9.figshare.c.3629942_d1.v1
title: Additional file 1: of Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha

description: Annotation of TBE sequences in Oxytricha micronuclear genome in gff format. (GFF 2.38 mb)
DOI: 10.6084/m9.figshare.c.3629933_d1.v1
title: MOESM3 of The antioxidative defense system is involved in the premature senescence in transgenic tobacco (Nicotiana tabacum NC89)

description: Additional file 3. Differentially expressed and identified unigenes in secondary metabolism signaling pathways.
DOI: 10.6084/m9.figshare.c.3629909_d6.v1
title: Additional file 3: of 
                     De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering

description: Candidate genes involved in circadian rhythm of radish. (XLSX 107 kb)
DOI: 10.6084/m9.figshare.c.3629930_d1.v1
title: Additional file 1: of Enlarged anterior cervical diskectomy and fusion in the treatment of severe localised ossification of the posterior longitudinal ligament

description: Raw Data. (XLS 31 kb)
DOI: 10.15468/dl.3myubh
title: Occurrence Download

description: A dataset containing 677 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sillago japonica Temminck & Schlegel, 1843",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 677 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036041-241126133413365/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.c.3629537_d4.v1
title: Additional file 5: Table S3. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

description: CAZymes. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3629537_d5.v1
title: Additional file 13: Table S8. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

description: Genbank and internal numbers (Rhynchosporium) for taxa used in this study. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3629537_d2.v1
title: Additional file 6: Table S4. of Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

description: (A) Cell wall degrading enzymes. (B) CWDE numbers according to their substrates. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.c.3629507_d3.v1
title: MOESM3 of Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway

description: Additional file 3. 13C Flux analysis of ST687 and non-producing strain ST1.
DOI: 10.6084/m9.figshare.c.3629507_d2.v1
title: MOESM2 of Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway

description: Additional file 2. Transcriptome analysis of ST687 compared to non-producing strain ST1.
DOI: 10.25345/c5dn4074c
title: MassIVE MSV000096667 - GNPS - Dataset Creation from GNPS Molcular Networking - b4bf8a487e324e8198b727ef8c47ed56
title: Extraction of medicinal plants Citrullus colocynthis using different organic solvents.
DOI: 10.6084/m9.figshare.c.3629474_d5.v1
title: Additional file 2: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

description: Spliced regions identified by RSR for the Dtt sample. This file contains all supplementary results for five test cases for the Dtt sample. (XLSX 2828 kb)
DOI: 10.6084/m9.figshare.c.3629474_d4.v1
title: Additional file 3: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

description: Statistics reported by RSR for 100 test cases for the Tg sample. This file contains all supplementary results for 100 test cases for the Tg sample. (XLSX 92 kb)
DOI: 10.6084/m9.figshare.c.3629474_d3.v1
title: Additional file 1: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

description: Spliced regions identified by RSR for the Tg sample. This file contains all supplementary results for five test cases for the Tg sample. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.c.3629474_d2.v1
title: Additional file 4: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

description: Statistics reported by RSR for 64 test cases for the Dtt sample. This file contains all supplementary results for 64 test cases for the Dtt sample. (XLSX 79 kb)
DOI: 10.6084/m9.figshare.c.3629474_d1.v1
title: Additional file 5: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

description: Total number of spliced regions identified by RSR in the human ENCODE RNA-Seq dataset. This file includes all supplementary results for number of supporting reads, splice length, range of supporting reads (spliced regions) identified by RSR in the human ENCODE RNA-Seq dataset. (XLSX 1411 kb)
DOI: 10.15468/dl.39y7n4
title: Occurrence Download

description: A dataset containing 3807 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (IDN.23_1, IDN.23.21_1)",
 "IucnRedListCategory is NT",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3807 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036043-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8s998p
title: Occurrence Download

description: A dataset containing 13250 species occurrences available in GBIF matching the query:
{
 "and" : [
 "FamilyKey is Magnoliaceae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is Specimen",
 "Country is China"
 ]
}

 The dataset includes 13250 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036042-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tbb9rt
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Thymus tomentosus var. virescens Coss."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036045-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xa58b5
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Thymus albicans Hoffmanns. & Link"
 ]
}

 The dataset includes 34 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036044-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kk48xy
title: Occurrence Download

description: A dataset containing 443 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pennahia argentata (Houttuyn, 1782)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 443 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036046-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f28pnt
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Thymus mastichina var. micranthus Boiss."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036047-241126133413365/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.c.3629159_d4.v1
title: Additional file 5: Table S2. of Complete depletion of primordial germ cells in an All-female fish leads to Sex-biased gene expression alteration and sterile All-male occurrence

description: DEGs between germ cell-depleted gynogenetic gonads and WT gynogenetic gonads at 25, 35, 45 and 60 dph, respectively. (XLSX 5697Â kb)