cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.uz66wf
title: Occurrence Download

description: A dataset containing 12818 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 {
 "or" : [
 "TaxonKey is Woodsia pulchella Bertol.",
 "TaxonKey is Sternbergia colchiciflora Waldst. & Kit.",
 "TaxonKey is Hydrocotyle vulgaris L.",
 "TaxonKey is Anthericum ramosum L.",
 "TaxonKey is Simethis mattiazzii (Vand.) Sacc.",
 "TaxonKey is Cerinthe glabra Mill.",
 "TaxonKey is Lappula deflexa",
 "TaxonKey is Gypsophila tomentosa L.",
 "TaxonKey is Maianthemum bifolium (L.) F.W.Schmidt",
 "TaxonKey is Erica vagans L.",
 "TaxonKey is Phyllodoce caerulea (L.) Bab.",
 "TaxonKey is Erodium foetidum (L.) Rothm., 1941",
 "TaxonKey is Hypericum elodes L.",
 "TaxonKey is Gagea pratensis (Pers.) Dumort.",
 "TaxonKey is Kosteletzkya pentacarpa Ledeb.",
 "TaxonKey is Orchis spitzelii Saut. ex W.D.J.Koch",
 "TaxonKey is Limonium costae (Willk.) Pignatti",
 "TaxonKey is Polygonum romanum subsp. gallicum (Raffaelli) Raffaelli & L.Villar",
 "TaxonKey is Aquilegia paui Font Quer",
 "TaxonKey is Salix foetida Sm.",
 "TaxonKey is Chrysosplenium alternifolium L.",
 "TaxonKey is Daphne alpina Sibth. & Sm.",
 "TaxonKey is Verbena supina L.",
 "TaxonKey is Asplenium obovatum var. obovatum",
 "TaxonKey is Asplenium selosii subsp. catalaunicum (Bol. & Vigo) P.Monts."
 ]
 }
 ]
}

 The dataset includes 12818 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011550-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7mydu3
title: Occurrence Download

description: A dataset containing 3581 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "CoordinateUncertaintyInMeters 0.0-99.0",
 "TaxonKey is Pyrus pyraster (L.) Burgsd.",
 "Year 1980-2024"
 ]
}

 The dataset includes 3581 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010866-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7s3fxj
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coffea fadenii Bridson"
 ]
}

 The dataset includes 46 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002493-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ec8n07
title: Occurrence Download

description: A dataset containing 1064707 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "Geometry POLYGON((-145.37 -63.09,-145.37 -11.38,-34.63 -11.38,-34.63 -63.09,-145.37 -63.09))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1064707 records from 568 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011550-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18419/darus-1666/100
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title: modelFFBE00B7C80C43D6B578E0FC56B67DEB12291.dat

description: :unav
DOI: 10.5281/zenodo.12913620
title: Neural Substrates for Early Data Reduction in Fast Vision: A Psychophysical Investigation

description: The name of each ‘.mat’ file reports the subject code, the condition (Baseline or Flicker), and the task (Sketch, Motion, or Orientation).

For Motion and Orientation tasks:

The matrices contain one row per trial and four columns:

o      Column 1: trial number

o      Column 2: tested contrast

o      Column 3: response (1 = left moving/oriented gabor, 2 = right moving/oriented gabor)

o      Column 4: correct response (1 = correct, 0 = wrong).

For the Sketch task:

The matrices contain one row per trial and seven columns:

o      Column 1: trial number

o      Column 2: tested contrast

o      Column 3: sketch number

o      Column 4: target image number

o      Column 5: distractor image number

o      Column 6: response (1 = left image, 2 = right image)

o      Column 7: correct response (1 = correct, 0 = wrong).
DOI: 10.5281/zenodo.12913621
title: Neural Substrates for Early Data Reduction in Fast Vision: A Psychophysical Investigation

description: The name of each ‘.mat’ file reports the subject code, the condition (Baseline or Flicker), and the task (Sketch, Motion, or Orientation).

For Motion and Orientation tasks:

The matrices contain one row per trial and four columns:

o      Column 1: trial number

o      Column 2: tested contrast

o      Column 3: response (1 = left moving/oriented gabor, 2 = right moving/oriented gabor)

o      Column 4: correct response (1 = correct, 0 = wrong).

For the Sketch task:

The matrices contain one row per trial and seven columns:

o      Column 1: trial number

o      Column 2: tested contrast

o      Column 3: sketch number

o      Column 4: target image number

o      Column 5: distractor image number

o      Column 6: response (1 = left image, 2 = right image)

o      Column 7: correct response (1 = correct, 0 = wrong).
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title: model2CD2C7268F96417881BFF5CA959D9402_tex7_1.dat

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DOI: 10.5281/zenodo.8215153
title: Systematic literature review database: responding to climate services in the context of drought

description: Literature review database associated to the work in Muller et al. 2024. For more details for the search keywords and selection criteria see the paper.

 

Muller, L. C., Schaafsma, M., Mazzoleni, M., & Van Loon, A. F. (2024). Responding to climate services in the context of drought: A systematic review. Climate Services, 35, 100493.
DOI: 10.5281/zenodo.8215154
title: Systematic literature review database: responding to climate services in the context of drought

description: Literature review database associated to the work in Muller et al. 2024. For more details for the search keywords and selection criteria see the paper.

 

Muller, L. C., Schaafsma, M., Mazzoleni, M., & Van Loon, A. F. (2024). Responding to climate services in the context of drought: A systematic review. Climate Services, 35, 100493.
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title: model8F18C2C86E094CE783396F662F6B405712291.dat

description: :unav
DOI: 10.18419/darus-1666/217
title: model0.dat_rnd.dat

description: :unav
DOI: 10.34740/kaggle/dsv/9038415
title: ⏳ endoflife.date database (duckdb)
DOI: 10.18419/darus-1666/218
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title: model32A2996302CE459B88BFBC5896E7B60D12291.dat

description: :unav
DOI: 10.5281/zenodo.10241527
title: Supplemental material for the manuscript "Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species".

description: Supplementary material for the manuscript “Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species”.

BreakpointsData.tar.xz contains:



Pairwise genome alignment files for Oikopleura, Ciona, Caenorhabditis, insects and muntjaks in GFF format in `inst/extdata/`.

dN / dS computation results in `inst/extdata/dNdS/`.

Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`.

OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade,

N3 the tunicates and N20 the _Ciona_ clade.

`BreakpointsData_3.11.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations.

The files needed to build the `BreakpointsData` package.


Oidioi_pairwise_v3.tar.gz contains:



The pairwise alignment files between genomes, in MAF format.

A copy of the Nextflow pipeline used to generate them.


oist-assembler.tar.gz contains:



A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`.

A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`.

A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`.


Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.

Oidioi_genomes.tar.gz contains:



For each genome, one file (`<genome>.fa`) containing the whole genome sequence and one directory (`<genome>`) containing each chromosome, scaffold or contig of the genome as a separate file.

For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object.


OrthoFinderRun.tar.xz contains:



A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.


Supplemental_Code.tar.gz contains:



A copy of <https://github.com/oist/LuscombeU_OikScrambling>, where the `.git` and `doc` directories were removed to save space.
description: The authors listed here are responsible for the upload to Zenodo.  Please refer to the manuscript for comprehensive information on the authors, their affiliations and their contributions.
DOI: 10.5281/zenodo.6601989
title: Supplemental material for the manuscript "Extreme genome scrambling in cryptic Oikopleura dioica species".

description: <strong>Supplementary material for Oikopleura scrambled genome study</strong> <em>BreakpointsData.tar.xz contains:</em> Pairwise genome alignment files in GFF format in `inst/extdata/Oidioi_pairwise_v3/`. dN / dS computation results in `inst/extdata/dNdS/`. Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`. OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade, N3 the tunicates and N20 the _Ciona_ clade. `BreakpointsData_3.9.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations. The files needed to build the `BreakpointsData` package. <em><strong>Oidioi_pairwise_v3.tar.gz contains:</strong></em> The pairwise alignment files between genomes, in MAF format. A copy of the Nextflow pipeline used to generate them. <em><strong>oist-assembler.tar.gz contains:</strong></em> A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`. A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`. A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`. <em>Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.</em> <em><strong>Oidioi_genomes.tar.gz contains:</strong></em> For each genome, one file (`&lt;genome&gt;.fa`) containing the whole genome sequence and one directory (`&lt;genome&gt;`) containing each chromosome, scaffold or contig of the genome as a separate file. For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object. <em><strong>OrthoFinderRun.tar.xz contains:</strong></em> A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.
description: The authors listed here are responsible for the upload to Zenodo. Please refer to the manuscript for comprehensive information on the authors, their affiliations and their contributions.
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