cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nb89tu
title: Occurrence Download

description: A dataset containing 5452 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Campylopterus falcatus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 5452 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085023-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.36a3vq
title: Occurrence Download

description: A dataset containing 63751 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Emberiza tahapisi)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 63751 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084995-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pe7mbu
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Putterlickia verrucosa (E.Mey. ex Sond.) Sim)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 55 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001950-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qjbwvb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Wallis and Futuna",
 "ScientificName is Epipremnum pinnatum"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005909-250525065834625/datasets/export for details.
DOI: 10.15468/dl.e4sr3y
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mayotte",
 "ScientificName is Christella dentata"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005910-250525065834625/datasets/export for details.
DOI: 10.3535/fme-f2q-w09
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rwf-jyb-zv6
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b3q-azz-w4k
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hk3-9mt-qkf
title: Lychniscosida Schrammen, 1903

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3v3-ttd-az1
title: Alasmidonta Say, 1818

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5by-ser-ewr
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hx3-p4m-68a
title: †Echinocorys Leske, 1778

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mzx-w2j-wsb
title: Cetacea Brisson, 1762

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vnr-nt6-00s
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gaq-1nw-4e3
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6bz-9n8-d64
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fsk-ajd-b5z
title: Ptychophylloceras

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9wk-2x8-cwc
title: Sus scrofa Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/scn-y6g-r0y
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3ly-pck-01r
title: Raja

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7lq-n9f-wkq
title: †Ptychophylloceras ptychoicum (Quenstedt, 1845)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5k4-gcn-bx6
title: †Entolium membranaceum (Nilsson, 1827)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rpq-cal-4a4
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/haq-e4f-kva
title: †Forbescythere kaasschieteri (Keij, 1957) Keen, 1976

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1sw-nrw-e35
title: †Columastrea striata (Goldfuss, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kj7-67g-53d
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kwq-ll6-10k
title: †Ptychophylloceras ptychoicum (Quenstedt, 1845)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/per-ylr-zww
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5nk-wz4-kmv
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c29-e4m-z6j
title: Chordata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c29-qzy-xq3
title: Spiticeras

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hbb-74l-613
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s1x-acp-1qa
title: Berriasella

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/95w-l04-nzw
title: Neolissoceras

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x50-y9l-kvc
title: †Hemipneustes striatoradiatus (Leske, 1778)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tjr-w0c-7h0
title: Ptychophylloceras

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xgx-hmt-4y2
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z5z-f31-y7h
title: Candona (Candona) Baird, 1845

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8mg-4l5-x83
title: Bison C. H. Smith, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v74-919-z97
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/531-vdz-axj
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7gd-3aw-7mh
title: Rangifer tarandus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8xq-gaz-tj8
title: Berriasella

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vk6-eyk-n4p
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p43-dy8-et0
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2g9-6q8-51l
title: †Conulus subrotundus Mantell, 1822

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xwy-2bz-b15
title: Bison C. H. Smith, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wm5-h86-jk8
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.h4cz2n
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.32_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Falco femoralis Temminck, 1822"
 ]
}

 The dataset includes 132 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000047-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m8agzn
title: Occurrence Download

description: A dataset containing 810 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Living Specimen)",
 {
 "or" : [
 "Geometry POLYGON((65 21,121 21,121 35,65 35,65 21))",
 "Geometry POLYGON((56 21,121 21,121 35,56 35,56 21))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cotoneaster microphyllus Wall. ex Lindl."
 ]
}

 The dataset includes 810 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000049-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60520/ieda/113456
title: Stable oxygen analysis of Cloverly vertebrate fossils

description: This dataset includes stable oxygen isotope (δ¹⁸O_phosphate) measurements from 112 fossil vertebrate specimens recovered from a microfossil bonebed in the Cloverly Formation (Carbon County, Montana), which dates to the mid-Cretaceous (Aptian–Albian). The specimens represent multiple vertebrate taxa, including aquatic, semi-aquatic, and terrestrial forms. Each record includes taxonomic identification, specimen number, skeletal element sampled, and δ¹⁸O_phosphate values reported in ‰ VSMOW.
DOI: 10.5281/zenodo.10679338
title: [Data] Monitoring of laser-induced fast recrystallization in SS-316L through synchrotron X-ray diffraction

description: In this paper, we perform laser heat treatment on a highly deformed 316L steel, and show that in-situ X-ray Diffraction (XRD) is a viable tool for the monitoring of fast recrystallization. X-ray signals are shown to reveal different stages of recrystallization, in particular the development of dislocation cells and the onset of nucleation. The data related to XRD analysis are uploaded here.
DOI: 10.5281/zenodo.10679339
title: [Data] Monitoring of laser-induced fast recrystallization in SS-316L through synchrotron X-ray diffraction

description: In this paper, we perform laser heat treatment on a highly deformed 316L steel, and show that in-situ X-ray Diffraction (XRD) is a viable tool for the monitoring of fast recrystallization. X-ray signals are shown to reveal different stages of recrystallization, in particular the development of dislocation cells and the onset of nucleation. The data related to XRD analysis are uploaded here.
DOI: 10.15468/dl.ab7wbv
title: Occurrence Download

description: A dataset containing 10289 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-2500.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus cerris L.",
 "Year 1950-2025"
 ]
}

 The dataset includes 10289 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000050-250424135625364/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.28738190.v27
title: Syllogistic reasoning pdf v1-2-3-4.rar

description: Logic and being
DOI: 10.5281/zenodo.11211925
title: Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance

description: The below data are associated with our paper entitled "Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance."

1) SNP-gene link predictions generated by pgBoost and existing methods SCENT (Sakaue et al. 2024 Nat Genet), Signac (Stuart et al. 2021 Nat Methods), ArchR (Granja et al. 2021 Nat Genet), and Cicero (Pliner et al. 2018 Mol Cell).

pgBoost_scores.tsv.gz contains linking predictions made by pgBoost.

constituent_method_scores.tsv.gz contains linking predictions made by constituent methods.

**NOTE: promoters (+/- 1kb from TSS) and candidate links >500kb are excluded from linking predictions (see manuscript)**

Linking scores and percentiles are reported for each method (pgBoost score, SCENT FDR, Signac correlation, ArchR correlation, Cicero co-accessibility). Rank percentiles are computed as: 1 - (rank / n). When multiple links receive the same score, they are assigned the percentile of the top rank. Links unscored by each method (denoted by zeros* in the linking score column) are assigned a percentile equivalent to the percent of links unscored by the focal method. See the Methods section of the paper for further details on computing linking scores and summarizing scores across cell types and data sets.

*Candidate links tested and assigned a co-accessibility of zero by the Cicero method are given a score of 1e-100 in the "Cicero" column to distinguish between unscored candidate links and candidate links assigned a partial correlation of zero (see Pliner et al. 2018 Mol Cell).

NOTE: The predictions associated with this release (version 2) were generated using an expanded set of data sets, an expanded training set, and corrected TSS coordinates.

2) GWAS-derived evaluation SNP-gene link evaluation set.

gwas_evaluation.tsv: GWAS-derived evaluation SNP-gene link evaluation set. Column 1 provides SNP coordinates in the format <chr-start-end>. This evaluation framework was proposed by Weeks et al. 2024 Nature Genetics based on fine-mapping results from Kanai et al. medrxiv (see Methods: Evaluation data sets of Dorans et al.). "True" links (gold = 1) are non-coding variants fine-mapped to a focal trait (PIP > 0.1) with a coding variant for exactly one candidate gene within 1 Mb attaining PIP > 0.5 for the same trait. "False" links (gold = 0) are candidate SNP-gene pairs involving a SNP with a "true" link. This file of SNP-gene links was adapted from credible set-gene links here (the "truth" column defines true/false links) by identifying SNPs with PIP > 0.1 within each credible set-gene link.
DOI: 10.5281/zenodo.11211926
title: Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance

description: SNP-gene link predictions associated with our paper titled "Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance," generated by pgBoost and constituent methods SCENT (Sakaue et al. 2024 Nat Genet), Signac (Stuart et al. 2021 Nat Methods), ArchR (Granja et al. 2021 Nat Genet), and Cicero (Pliner et al. 2018 Mol Cell).

pgBoost_scores.tsv.gz contains linking predictions made by pgBoost.

constituent_method_scores.tsv.gz contains linking predictions made by constituent methods.

Linking scores and percentiles are reported for each method (pgBoost score, SCENT FDR, Signac correlation, ArchR correlation, Cicero co-accessibility). Rank percentiles are computed as: 1 - (rank / n). When multiple links receive the same score, they are assigned the percentile of the top rank. Links unscored by each method (denoted by zeros* in the linking score column) are assigned a percentile equivalent to the percent of links unscored by the focal method. See the Methods section of the paper for further details on computing linking scores and summarizing scores across cell types and data sets.

*Candidate links tested and assigned a co-accessibility of zero by the Cicero method are given a score of 1e-100 in the "Cicero" column to distinguish between unscored candidate links and candidate links assigned a co-accessibility of zero (see Pliner et al. 2018 Mol Cell).
DOI: 10.5281/zenodo.14862747
title: Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance

description: SNP-gene link predictions associated with our paper titled "Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance," generated by pgBoost and existing methods SCENT (Sakaue et al. 2024 Nat Genet), Signac (Stuart et al. 2021 Nat Methods), ArchR (Granja et al. 2021 Nat Genet), and Cicero (Pliner et al. 2018 Mol Cell).

pgBoost_scores.tsv.gz contains linking predictions made by pgBoost.

constituent_method_scores.tsv.gz contains linking predictions made by constituent methods.

Linking scores and percentiles are reported for each method (pgBoost score, SCENT FDR, Signac correlation, ArchR correlation, Cicero co-accessibility). Rank percentiles are computed as: 1 - (rank / n). When multiple links receive the same score, they are assigned the percentile of the top rank. Links unscored by each method (denoted by zeros* in the linking score column) are assigned a percentile equivalent to the percent of links unscored by the focal method. See the Methods section of the paper for further details on computing linking scores and summarizing scores across cell types and data sets.

*Candidate links tested and assigned a co-accessibility of zero by the Cicero method are given a score of 1e-100 in the "Cicero" column to distinguish between unscored candidate links and candidate links assigned a partial correlation of zero (see Pliner et al. 2018 Mol Cell).

NOTE: The predictions associated with this release (version 2) were generated using an expanded set of data sets, an expanded training set, and corrected SNP-gene distances.
DOI: 10.5281/zenodo.14957607
title: Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance

description: The below data are associated with our paper entitled "Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance."

1) SNP-gene link predictions generated by pgBoost and existing methods SCENT (Sakaue et al. 2024 Nat Genet), Signac (Stuart et al. 2021 Nat Methods), ArchR (Granja et al. 2021 Nat Genet), and Cicero (Pliner et al. 2018 Mol Cell).

pgBoost_scores.tsv.gz contains linking predictions made by pgBoost.

constituent_method_scores.tsv.gz contains linking predictions made by constituent methods.

**NOTE: promoters (+/- 1kb from TSS) and candidate links >500kb are excluded from linking predictions (see manuscript)**

Linking scores and percentiles are reported for each method (pgBoost score, SCENT FDR, Signac correlation, ArchR correlation, Cicero co-accessibility). Rank percentiles are computed as: 1 - (rank / n). When multiple links receive the same score, they are assigned the percentile of the top rank. Links unscored by each method (denoted by zeros* in the linking score column) are assigned a percentile equivalent to the percent of links unscored by the focal method. See the Methods section of the paper for further details on computing linking scores and summarizing scores across cell types and data sets.

*Candidate links tested and assigned a co-accessibility of zero by the Cicero method are given a score of 1e-100 in the "Cicero" column to distinguish between unscored candidate links and candidate links assigned a partial correlation of zero (see Pliner et al. 2018 Mol Cell).

NOTE: The predictions associated with this release (version 2) were generated using an expanded set of data sets, an expanded training set, and corrected TSS coordinates.

2) GWAS-derived evaluation SNP-gene link evaluation set.

gwas_evaluation.tsv: GWAS-derived evaluation SNP-gene link evaluation set. Column 1 provides SNP coordinates in the format <chr-start-end>. This evaluation framework was proposed by Weeks et al. 2024 Nature Genetics based on fine-mapping results from Kanai et al. medrxiv (see Methods: Evaluation data sets of Dorans et al.). "True" links (gold = 1) are non-coding variants fine-mapped to a focal trait (PIP > 0.1) with a coding variant for exactly one candidate gene within 1 Mb attaining PIP > 0.5 for the same trait. "False" links (gold = 0) are candidate SNP-gene pairs involving a SNP with a "true" link. This file of SNP-gene links was adapted from credible set-gene links here (the "truth" column defines true/false links) by identifying SNPs with PIP > 0.1 within each credible set-gene link.
DOI: 10.15468/dl.c83kxn
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Poterium creticum (Hayek) Holub",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0293344-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c86y7v
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rubus atrovinosus H.E.Weber",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0291026-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c92na7
title: Occurrence Download

description: A dataset containing 4540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chorispora tenella (Pall.) DC.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4540 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0293794-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.