cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9sm2gb
title: Occurrence Download

description: A dataset containing 4620 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eupatorium lindleyanum DC."
 ]
}

 The dataset includes 4620 records from 153 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043574-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cyi5ot
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Bolivia (Plurinational State of)",
 "Country is Colombia",
 "Country is Venezuela (Bolivarian Republic of)"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Poteranthera Bong.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038900-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ygmgza
title: Occurrence Download

description: A dataset containing 4993 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Equus quagga Boddaert, 1785, Equus quagga Gmelin, 1788, Equus quagga chapmani Layard, 1865, Equus quagga boehmi Matschie, 1892, Equus quagga quagga, Equus quagga borensis Lönnberg, 1921, Equus quagga crawshayi de Winton, 1896, Equus quagga burchellii (Gray, 1824))"
 ]
}

 The dataset includes 4993 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043567-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lxbac2
title: Occurrence Download

description: A dataset containing 16409 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potamogeton lucens L.",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 16409 records from 194 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038901-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5jx4c
title: Occurrence Download

description: A dataset containing 3876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Equisetales"
 ]
}

 The dataset includes 3876 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256200-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vadrgr
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erythroxylum moonii Hochr."
 ]
}

 The dataset includes 34 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043675-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qzwwj2
title: Occurrence Download

description: A dataset containing 236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-92.63672 -44.71875,-27.59766 -44.71875,-27.59766 23.48438,-92.63672 23.48438,-92.63672 -44.71875))",
 "TaxonKey is Chironius fuscus (Linnaeus, 1758)"
 ]
}

 The dataset includes 236 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030023-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fiylgc
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Mitu salvini Reinhardt, 1879"
 ]
}

 The dataset includes 25 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038902-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6f6d27
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erica flanaganii Bolus"
 ]
}

 The dataset includes 25 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043676-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jyatc4
title: Occurrence Download

description: A dataset containing 726 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pygophora"
 ]
}

 The dataset includes 726 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0263756-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ab2lqr
title: Occurrence Download

description: A dataset containing 42254 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Fossil",
 "BasisOfRecord is Literature Occurrence"
 ]
 },
 "HasCoordinate is true",
 {
 "or" : [
 "TaxonKey is Crotonogyne Müll.Arg.",
 "TaxonKey is Deuteromallotus Pax & K.Hoffm.",
 "TaxonKey is Discoglypremna Prain",
 "TaxonKey is Ditta Griseb.",
 "TaxonKey is Endospermum Benth.",
 "TaxonKey is Erythrococca Benth.",
 "TaxonKey is Givotia Griff.",
 "TaxonKey is Grossera Pax",
 "TaxonKey is Hamilcoa Prain",
 "TaxonKey is Homonoia Lour.",
 "TaxonKey is Klaineanthus Pierre ex Prain",
 "TaxonKey is Lasiocroton Griseb.",
 "TaxonKey is Macaranga Thouars",
 "TaxonKey is Mallotus Lour.",
 "TaxonKey is Manniophyton Müll.Arg.",
 "TaxonKey is Neoboutonia Müll.Arg.",
 "TaxonKey is Neoscortechinia Pax",
 "TaxonKey is Neotrewia Pax & K.Hoffm.",
 "TaxonKey is Orfilea Baill.",
 "TaxonKey is Pausandra Radlk.",
 "TaxonKey is Pimeleodendron Müll.Arg., 1866",
 "TaxonKey is Plagiostyles Pierre",
 "TaxonKey is Pseudagrostistachys Pax & K.Hoffm.",
 "TaxonKey is Ptychopyxis Miq.",
 "TaxonKey is Ricinodendron Müll.Arg.",
 "TaxonKey is Sandwithia Lanj.",
 "TaxonKey is Spathiostemon Blume",
 "TaxonKey is Suregada Roxb. ex Rottler",
 "TaxonKey is Tannodia Baill.",
 "TaxonKey is Tapoides Airy Shaw",
 "TaxonKey is Tetrorchidium Poepp.",
 "TaxonKey is Trewia L., 1753",
 "TaxonKey is Wetria Baill.",
 "TaxonKey is Ateleia (DC.) D.Dietr.",
 "TaxonKey is Myroxylon L.f.",
 "TaxonKey is Garryaceae",
 "TaxonKey is Griselinia G.Forst.",
 "TaxonKey is Gyrostemon Desf.",
 "TaxonKey is Tersonia Moq.",
 "TaxonKey is Hanguana Blume",
 "TaxonKey is Broussaisia Gaudich."
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 42254 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038903-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h3mm93
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriolaena richardii (Baill.) Dorr"
 ]
}

 The dataset includes 55 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043677-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ntb24h
title: Occurrence Download

description: A dataset containing 544 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Issue is Geodetic datum assumed WGS84",
 "TaxonKey is Pinus armandii Franch."
 ]
}

 The dataset includes 544 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256228-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bsjiq9
title: Occurrence Download

description: A dataset containing 130968 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriophorum vaginatum L."
 ]
}

 The dataset includes 130968 records from 371 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038904-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.su4jrq
title: Occurrence Download

description: A dataset containing 227 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erythroxylum novocaledonicum O.E.Schulz"
 ]
}

 The dataset includes 227 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043686-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yvh4va
title: Occurrence Download

description: A dataset containing 3216 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Occurrence data of ants (Hymenoptera: Formicidae) in the Zoological collection of National Museums of Kenya"
 ]
}

 The dataset includes 3216 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038905-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5dcw3p
title: Occurrence Download

description: A dataset containing 702682 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Tussilago farfara)"
 ]
}

 The dataset includes 702682 records from 1899 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054671-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15621076
title: Axion
DOI: 10.5281/zenodo.15621077
title: Axion
DOI: 10.7266/n73f4mmv
title: Dataset for: Phase and sedimentation behavior of oil (octane) dispersions in the presence of model mineral aggregates
DOI: 10.15468/dl.ufffnu
title: Occurrence Download

description: A dataset containing 739851 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-05-14",
 "EventDate is less than or equal to 2025-06-13",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 739851 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029859-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ex42gf
title: Occurrence Download

description: A dataset containing 20083 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "Geometry POLYGON((-173.90328 0.07381,-168.04178 0.07381,-65.32262 14.02832,-45.93092 11.68227,-58.51644 26.03922,-7.67028 84.89265,-61.94545 89.35278,-164.83887 86.9506,-173.90328 4.07536,-173.90328 0.07381))",
 "TaxonKey is Cytisus scoparius (L.) Link"
 ]
}

 The dataset includes 20083 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008454-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13913509
title: Electromagnetic Coil Optimization for Reduced Lorentz Forces

description: This is the dataset and code used for the paper "Electromagnetic Coil Optimization for Reduced Lorentz Forces" by Hurwitz et al. For the main file itself, see the 'analysis.ipynb' Jupyter notebook.
DOI: 10.5281/zenodo.13913510
title: Electromagnetic Coil Optimization for Reduced Lorentz Forces

description: This is the dataset and code used for the paper "Electromagnetic Coil Optimization for Reduced Lorentz Forces" by Hurwitz et al. For the main file itself, see the 'analysis.ipynb' Jupyter notebook.
DOI: 10.15468/dl.frqhmb
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Peru, Ecuador, French Guiana, Colombia, Bolivia (Plurinational State of))",
 "OccurrenceStatus is Present",
 "TaxonKey is Micrurus surinamensis (Cuvier, 1816)",
 "Year 2023-2024"
 ]
}

 The dataset includes 44 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008455-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6c39nu
title: Occurrence Download

description: A dataset containing 2986 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Specimen)",
 "Continent is North America",
 "OccurrenceStatus is Present",
 "TaxonKey is Tardigrada"
 ]
}

 The dataset includes 2986 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008456-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p442fz
title: Occurrence Download

description: A dataset containing 11825 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hylesinus varius (J.C.Fabricius, 1775)",
 "OccurrenceStatus is Present",
 "Country is not null",
 "Year is not null"
 ]
}

 The dataset includes 11825 records from 270 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008457-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s4vcph
title: Occurrence Download

description: A dataset containing 6898 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trypodendron signatum (J.C.Fabricius, 1792)",
 "OccurrenceStatus is Present",
 "Country is not null",
 "Year is not null"
 ]
}

 The dataset includes 6898 records from 183 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008460-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.27btec
title: Occurrence Download

description: A dataset containing 8031 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trachys minutus (Linnaeus, 1758)",
 "OccurrenceStatus is Present",
 "Country is not null",
 "Year is not null"
 ]
}

 The dataset includes 8031 records from 305 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008458-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qca3rk
title: Occurrence Download

description: A dataset containing 11831 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hylesinus varius (J.C.Fabricius, 1775)",
 "OccurrenceStatus is Present",
 "Country is not null",
 "Year is not null"
 ]
}

 The dataset includes 11831 records from 271 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008459-241007104925546/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.25917910.v1
title: Data, metadata, and analysis code for Johnson et al. 'Emergence of Black Spot Syndrome in Caribbean reefs: A century of fish collections reveal long-term increases in <i>Scaphanocephalus</i> infection'

description: Contains data, metadata, and analysis code in R for Johnson, P. T. J., Malawauw, R. J., Piaskowy, J., Calhoun, D. M., Kohl, Z., ter Horst, L. J. V. and D. Zelmer. Emergence of Black Spot Syndrome in Caribbean reefs: A century of fish collections reveal long-term increases in <i>Scaphanocephalus</i>infection. Proceedings of the Royal Society B.
DOI: 10.6084/m9.figshare.27212565.v1
title: Composite alignment

description: This is the composite alignment for phylogenetic analyses of a new Xenodisymella species, namely <b><i>Xenodidymella quercicola</i></b>.
DOI: 10.6084/m9.figshare.27212565
title: Composite alignment

description: This is the composite alignment for phylogenetic analyses of a new Xenodisymella species, namely <b><i>Xenodidymella quercicola</i></b>.
DOI: 10.5281/zenodo.8179264
title: Warming could shift the phenological responses of benthic microalgae in temperate intertidal zones

description: Intertidal mudflats colonized by sediment-dwelling microphytobenthos deliver a wide range of ecosystem services. Here we simulate the response of microphytobenthos exposed to changes in light, temperature, and sea level conditions on a temperate tidal mudflat located along the French Atlantic coast in Northwestern Europe predicted by the Intergovernmental Panel on Climate Change. Without sea level rise, microphytobenthos benefit from the balancing effect of net primary production fluctuations, experiencing an increase in winter and a decrease in summer. Under the worst emissions scenario, microphytobenthos bloom up to 14 days earlier in spring and 5 days later in fall, thereby extending the low-level microphytobenthos biomass period by an additional 3 weeks in summer. Sea level rise reduces light exposure leading to a pronounced decline in microphytobenthos under the medium-low emissions and worst emissions scenarios. We provide evidence that the anticipated warmer climate and sea level rise will have an impact on microphytobenthos, potentially triggering cascading effects across the entire food web and disrupting ecosystem services.
DOI: 10.5281/zenodo.13900917
title: Machine learning reveals the diversity of human 3D chromatin contact patterns (example predictions genome wide)

description: Example data for the paper: Machine learning reveals the diversity of human 3D chromatin contact patterns

GitHub: https://github.com/erin-n-gilbertson/3DGenome-diversity/tree/main

biorXiv: https://www.biorxiv.org/content/10.1101/2023.12.22.573104v1.full

Manuscript accepted at Molecular Biology and Evolution

Of primary interest will be the example predictions genome wide for hg38 reference, human-archaic hominin ancestor and most divergent 1KG individual per genome along with the Jupyter notebook tutorial for making your own Akita predictions given any input 1MB sequence.





bin: contains python script for and qsub array shell script for generating example predictions. These scripts can be modified to take in any fasta files as input.

akita_predictions: contains both Akita prediction output arrays and SVG files with predicted contact maps for the hg38 reference, human-archaic hominin ancestor and most divergent 1KG individual in each of 4,873 1MB windows

anc_window_spearman.csv: spearman correlation between each 1KG individual and the ancestor for each 1MB window. To calculate 3D divergence subtract these values from 1.

basenji: basenji dir from their github, necessary in the directory to run predictions - https://github.com/calico/basenji/tree/master

genomes: fasta genomes for hg38 reference and human-archaic hominin ancestor used to make akita predictions

divergent_windows: variants and expected divergence distributions for 392 more divergent than expected windows. Defined in the manuscript as windows where 3D divergence between 1KG indiivudals and the ancestor is greater than what would be expected based on sequence divergence. See manuscript Fig. S9 for more details. 

windows.txt: 4,873 1MB genomic windows with 100% coverage in hg38 used for Akita predictions

making_examples.ipynb: jupyter notebook with tutorial instructions for making Akita predictions on any human genome sequence.
DOI: 10.5281/zenodo.13900918
title: Machine learning reveals the diversity of human 3D chromatin contact patterns (example predictions genome wide)

description: Example data for the paper: Machine learning reveals the diversity of human 3D chromatin contact patterns

GitHub: https://github.com/erin-n-gilbertson/3DGenome-diversity/tree/main

biorXiv: https://www.biorxiv.org/content/10.1101/2023.12.22.573104v1.full

Manuscript accepted at Molecular Biology and Evolution

Of primary interest will be the example predictions genome wide for hg38 reference, human-archaic hominin ancestor and most divergent 1KG individual per genome along with the Jupyter notebook tutorial for making your own Akita predictions given any input 1MB sequence.





bin: contains python script for and qsub array shell script for generating example predictions. These scripts can be modified to take in any fasta files as input.

akita_predictions: contains both Akita prediction output arrays and SVG files with predicted contact maps for the hg38 reference, human-archaic hominin ancestor and most divergent 1KG individual in each of 4,873 1MB windows

anc_window_spearman.csv: spearman correlation between each 1KG individual and the ancestor for each 1MB window. To calculate 3D divergence subtract these values from 1.

basenji: basenji dir from their github, necessary in the directory to run predictions - https://github.com/calico/basenji/tree/master

genomes: fasta genomes for hg38 reference and human-archaic hominin ancestor used to make akita predictions

divergent_windows: variants and expected divergence distributions for 392 more divergent than expected windows. Defined in the manuscript as windows where 3D divergence between 1KG indiivudals and the ancestor is greater than what would be expected based on sequence divergence. See manuscript Fig. S9 for more details. 

windows.txt: 4,873 1MB genomic windows with 100% coverage in hg38 used for Akita predictions

making_examples.ipynb: jupyter notebook with tutorial instructions for making Akita predictions on any human genome sequence.
DOI: 10.15468/dl.adqfaw
title: Occurrence Download

description: A dataset containing 6898 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trypodendron signatum (J.C.Fabricius, 1792)",
 "OccurrenceStatus is Present",
 "Country is not null",
 "Year is not null"
 ]
}

 The dataset includes 6898 records from 183 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008463-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.