cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.kd5ujz
title: Occurrence Download

description: A dataset containing 934 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Geodetic datum assumed WGS84",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus terrestris (Linnaeus, 1758)"
 ]
}

 The dataset includes 934 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067034-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yalmtl
title: Occurrence Download

description: A dataset containing 415223 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cirsium vulgare (Savi) Ten."
 ]
}

 The dataset includes 415223 records from 919 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008868-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sc6c2a
title: Occurrence Download

description: A dataset listing the 2897 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-0.16307 53.67478,0.25938 53.67478,0.25938 53.97944,-0.16307 53.97944,-0.16307 53.67478))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 2897 records were derived from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008890-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-144953
title: Renewal, no. 55 (Feb./Mar. 1975)

description: [description english/roman)] Renewal, no. 55 (Feb./Mar. 1975). Published six times per year.
DOI: 10.15468/dl.6lkg07
title: Occurrence Download

description: A dataset containing 7344 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zalophus californianus (Lesson, 1828)"
 ]
}

 The dataset includes 7344 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005022-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xpgakp
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paraleucothoe flindersi (Stebbing, 1888)"
 ]
}

 The dataset includes 56 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127963-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x6j5ny
title: Occurrence Download

description: A dataset containing 7622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Egretta eulophotes",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 7622 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0070389-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-22527
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council
DOI: 10.25549/pcra-c14-22547
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council
DOI: 10.15468/dl.7yfv59
title: Occurrence Download

description: A dataset containing 1414 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Drymarchon melanurus (Duméril, Bibron & Duméril, 1854)"
 ]
}

 The dataset includes 1414 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033398-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uxa8tr
title: Occurrence Download

description: A dataset containing 1052 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Venturia inaequalis (Cooke) G.Winter"
 ]
}

 The dataset includes 1052 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0127972-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d4uqk8
title: Occurrence Download

description: A dataset containing 749 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erodius Fabricius, 1775"
 ]
}

 The dataset includes 749 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021678-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.7527905
title: Dataset for "High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with higher transcription, gene body hypomethylation, and proximity to transposable elements"

description: Data generated associated with understanding the features of NLRs in Arabidopsis Col-0. Contains: -all_gene_table.xslx: % CG gene body methylation, log2(TPM), and distance to nearest TE for all genes -working_table.xslx: cluster status, N-terminal domain class, and genome position of NLRs -The CHH, CHG, and CG bigwig files -Simulated RNAseq reads -iTOL annotation files
DOI: 10.25549/pcra-c14-22674
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council
DOI: 10.15468/dl.mj8ge4
title: Occurrence Download

description: A dataset containing 417 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alpinia galanga (L.) Willd."
 ]
}

 The dataset includes 417 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005022-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8411396
title: Dataset for "High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with distinct genomic and epigenomic features "

description: Data generated associated with understanding the features of NLRs in Arabidopsis Col-0. Contains: -all_gene_table.xslx: %CG gene body methylation, log2(TPM), distance to nearest TE, Pi (normalized by bp and by effective site), Tajima's D for all genes -working_table.xslx: cluster status, N-terminal domain class, and genome position of NLRs -Athaliana_NLR_entropy: Shannon entropy calculated per sequence of Athaliana NLRs -egglib_window_stats: Pi and D calculated over 300bp windows, 75bp step of all NLRs -popgen_per_domain: Pi, D, PiS, and PiN calculated by domain of all NLRs -positive_selection: proportion of sites under positive selection estimated by MEME and FEL at a posterior probability &gt; 0.95, corrected for multiple hypothesis testing -nlr_aa_annotation: alignment position based annotation of domains -nlrome_IDs.txt: IDs of accessions used to make VCF files for whole genome popgen analysis -The CHH, CHG, and CG bigwig files -Simulated RNAseq reads generated using Polyester -iTOL annotation files
DOI: 10.25549/pcra-c14-22615
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council
DOI: 10.15468/dl.8edef6
title: Occurrence Download

description: A dataset containing 2657 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters is less than or equal to 10000.0",
 "Geometry POLYGON((-125.20394 26.81355,-62.48421 26.81355,-62.48421 48.55001,-125.20394 48.55001,-125.20394 26.81355))",
 "TaxonKey is Bromus tectorum L."
 ]
}

 The dataset includes 2657 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021658-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxheey
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diminovula culmen (C.N.Cate, 1973)"
 ]
}

 The dataset includes 100 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086172-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10530531
title: Dataset for "High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features"

description: This repository contains intermediate data for the publication, "High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features". Detailed descriptions of the methods, analyses, and generation of these files are available there. 

This repository contains the following files: 



all_gene_multi_tissue_methylation.csv: Arabidopsis Col-0 %CG methylation across cauline leaf, embryo, flower bud, and rosette leaf tissue as described in Williams et. al 2022.

all_gene_multi_tissue_expression.csv: Arabidopsis Col-0 expression across 52 samples as described in Mergner et. al 2020

all_gene_table.csv: Gene name, HV status (hv, non-hv, or all_genes), log2(TPM+1) and %CG methylation from rosette leaf tissue, distance to nearest TE, Pi, and Tajima's D for all genes in Arabidopsis Col-0 

NLR_gene_table.csv: the same information in all_gene_table.csv, subset to NLRs. Additional information only relevant to NLRs includes cluster_type (singleton, major, or minor), cluster (name of cluster, if exists), Nterm domain, Clade from phylogenetic analysis in Prigozhin and Krasileva 2021, PiN, PiS, PiN/PiS, and distance to nearest NLR. Mutation.Probability.Score from Monroe et. al 2020. 

Atha_NLR_common_names.csv: common names matched to gene IDs used in this analysis 

Athaliana_NLR_Entropy.tsv: Shannon entropy calculated per gene in reference to Col-0 NLRs.  

popgen_per_domain.csv: NLR specific, domain level statistics. Alignment coordinates of domain annotations are found in nlr_aa_annotation.csv

egglib_window_stats.csv: contains the results of the sliding window analysis for NLRs. Statistics were calculated on 300bp windows with a step size of 75bp. The nuc_midpoint is the midpoint of that window. 

nlr_aa_annotation.csv: Codon alignment coordiates of major domains across NLRs using majority vote across accessions. NB-ARC, TIR, and CC annotations were collected from previous work (Van de Weyer et. al, 2019), and LRR annotations were determined using LRRpredictor (Martin et. al, 2020). 

nlrome_IDs.txt: list of NLRome IDs (Van de Weyer et. al, 2019) used to make VCF files for the whole genome popgen analysis

popgen_per_domain.csv: Per domain population genetics statistics calculated from alignments of NLRs using egglib

positive_selection.csv: Sites under pervasive diversifying selection were identified using FEL (Kosakovsky Pond & Frost, 2005) and sites under episodic diversifying selection were identified using MEME (Murrell et al, 2012) using the internal branches of the phylogeny (Pond et al, 2006; Avanzato et. al, 2019). Value is the percentage of codons under positive selection determined by 95% confidence.
DOI: 10.5281/zenodo.7527904
title: Dataset for "High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features"

description: This repository contains intermediate data for the publication, "High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features". Detailed descriptions of the methods, analyses, and generation of these files are available there. 

This repository contains the following files: 



all_gene_multi_tissue_methylation.csv: Arabidopsis Col-0 %CG methylation across cauline leaf, embryo, flower bud, and rosette leaf tissue as described in Williams et. al 2022.

all_gene_multi_tissue_expression.csv: Arabidopsis Col-0 expression across 52 samples as described in Mergner et. al 2020

all_gene_table.csv: Gene name, HV status (hv, non-hv, or all_genes), log2(TPM+1) and %CG methylation from rosette leaf tissue, distance to nearest TE, Pi, and Tajima's D for all genes in Arabidopsis Col-0 

NLR_gene_table.csv: the same information in all_gene_table.csv, subset to NLRs. Additional information only relevant to NLRs includes cluster_type (singleton, major, or minor), cluster (name of cluster, if exists), Nterm domain, Clade from phylogenetic analysis in Prigozhin and Krasileva 2021, PiN, PiS, PiN/PiS, and distance to nearest NLR. Mutation.Probability.Score from Monroe et. al 2020. 

Atha_NLR_common_names.csv: common names matched to gene IDs used in this analysis 

Athaliana_NLR_Entropy.tsv: Shannon entropy calculated per gene in reference to Col-0 NLRs.  

popgen_per_domain.csv: NLR specific, domain level statistics. Alignment coordinates of domain annotations are found in nlr_aa_annotation.csv

egglib_window_stats.csv: contains the results of the sliding window analysis for NLRs. Statistics were calculated on 300bp windows with a step size of 75bp. The nuc_midpoint is the midpoint of that window. 

nlr_aa_annotation.csv: Codon alignment coordiates of major domains across NLRs using majority vote across accessions. NB-ARC, TIR, and CC annotations were collected from previous work (Van de Weyer et. al, 2019), and LRR annotations were determined using LRRpredictor (Martin et. al, 2020). 

nlrome_IDs.txt: list of NLRome IDs (Van de Weyer et. al, 2019) used to make VCF files for the whole genome popgen analysis

popgen_per_domain.csv: Per domain population genetics statistics calculated from alignments of NLRs using egglib

positive_selection.csv: Sites under pervasive diversifying selection were identified using FEL (Kosakovsky Pond & Frost, 2005) and sites under episodic diversifying selection were identified using MEME (Murrell et al, 2012) using the internal branches of the phylogeny (Pond et al, 2006; Avanzato et. al, 2019). Value is the percentage of codons under positive selection determined by 95% confidence.
DOI: 10.25549/pcra-c14-22696
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council
DOI: 10.15468/dl.zahw73
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-123.73661 21.48778,-74.64970 21.48778,-74.64970 41.13134,-123.73661 41.13134,-123.73661 21.48778))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pupilla muscorum (Linnaeus, 1758)"
 ]
}

 The dataset includes 62 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059873-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sazcxv
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.87468 9.1196,-79.81077 9.1196,-79.81077 9.18686,-79.87468 9.18686,-79.87468 9.1196))",
 "HasCoordinate is true",
 "TaxonKey is Sphingidae"
 ]
}

 The dataset includes 57 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021684-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d448ur
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-88.3170992999999953 41.7654799000000025, -88.3170992999999953 41.7662698800000030, -88.3170992999999953 41.7674548500000000, -88.3170992999999953 41.7682448300000004, -88.3170992999999953 41.7693639599999997, -88.3170992999999953 41.7708780899999965, -88.3170992999999953 41.7717339000000010, -88.3170992999999953 41.7728530400000011, -88.3170992999999953 41.7742355000000032, -88.3152618299999972 41.7742355000000032, -88.3140149700000023 41.7742355000000032, -88.3119149999999991 41.7742355000000032, -88.3105369000000024 41.7742355000000032, -88.3105369000000024 41.7732480299999978, -88.3105369000000024 41.7717339000000010, -88.3105369000000024 41.7699564500000022, -88.3105369000000024 41.7691006399999978, -88.3105369000000024 41.7681789900000027, -88.3105369000000024 41.7671256900000003, -88.3105369000000024 41.7654799000000025, -88.3115868799999930 41.7654799000000025, -88.3129649899999976 41.7654799000000025, -88.3145399600000047 41.7654799000000025, -88.3160493200000047 41.7654799000000025, -88.3170992999999953 41.7654799000000025))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 206 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086119-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-22692
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council
DOI: 10.15468/dl.pm8fo9
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Madagascar",
 "Year 1960-2018",
 "HasCoordinate is true",
 "TaxonKey is Prolemur simus (Gray, 1870)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 24 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006112-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-22658
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council
DOI: 10.15468/dl.nmk4rw
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diminovula alabaster (Reeve, 1865)"
 ]
}

 The dataset includes 129 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086169-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tck54t
title: Occurrence Download

description: A dataset containing 15448 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lycorma delicatula (White, 1845)"
 ]
}

 The dataset includes 15448 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021674-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g3flqu
title: Occurrence Download

description: A dataset containing 2189 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myrcianthes fragrans (Sw.) McVaugh"
 ]
}

 The dataset includes 2189 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006112-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-22654
title: Letters of Mundell, Thomas, Secretary of Home Reference Missionary Council, PMU, June 1925-July 1927

description: [description english/roman)] Pentecostal Missionary Union [PMU]/Assemblies of God [AoG] Home Reference Missionary Council outgoing correspondence from Home Reference Missionary Council secretary Thomas Mundell, including index for correspondence 109 pages and correspondence 2026 pages. Outgoing letters sent by Mundell on behalf of Assemblies of God [AoG] Home Reference Missionary Council