cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2pmdd4
title: CCDC 2491296: Experimental Crystal Structure Determination

description: Related Article: Jiyong Li, Songyang Li, Cuijuan Zhang, Liankun Ai, Jiaxiang Chu|2025|Inorg.Chem.|||doi:10.1021/acs.inorgchem.5c04581
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.mg9mhd
title: Occurrence Download

description: A dataset containing 59662 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "PublishingOrg is 1928bdf0-f5d2-11dc-8c12-b8a03c50a862",
 "TaxonKey is Lutra lutra"
 ]
}

 The dataset includes 59662 records from 722 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047398-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17899935
title: Benchmarks accompanying "Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks"

description: Delphy paper data
Datasets, scripts for analyzing them, and scripts to generate figures.

Although these scripts were last successfully run in late 2025 to prepare, execute and analyze the Delphy and BEAST2 runs, there is no guarantee that they will run perfectly in the future and/or on your machine. We do not intend to maintain these scripts moving forward. Instead, the aim of this repo is to be living documentation of all the details of the runs and plots.
DOI: 10.5517/ccdc.csd.cc2qdj8y
title: CCDC 2514480: Experimental Crystal Structure Determination

description: Related Article: Kwang-Sei Lee|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.17899934
title: Benchmarks accompanying "Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks"

description: Delphy paper data
Datasets, scripts for analyzing them, and scripts to generate figures.

Although these scripts were last successfully run in late 2025 to prepare, execute and analyze the Delphy and BEAST2 runs, there is no guarantee that they will run perfectly in the future and/or on your machine. We do not intend to maintain these scripts moving forward. Instead, the aim of this repo is to be living documentation of all the details of the runs and plots.
DOI: 10.6084/m9.figshare.30861923
title: Dataset

description: Calificaciones de estudiantes
DOI: 10.6084/m9.figshare.30861923.v1
title: Dataset

description: Calificaciones de estudiantes
DOI: 10.34847/nkl.abe2875s
title: Base de données des collages féministes parisiens (2019–2024). Analyse de la production des collages féministes à Paris (par Collages Féminicides Paris)

description: La base de données est issue de la thèse doctorale "Géographie de l'invisible : les territoires de la mémoire des femmes". Elle a été construite à partir des photographies des collages féminicides réalisées et transmises par les activistes du mouvement Collages Féminicides Paris (CFP) entre septembre 2019 et août 2024. Les images proviennent de plusieurs sources complémentaires : les publications Instagram du compte officiel du mouvement, les publications Instagram des trois photographes associé·es au collectif à ses débuts, les photographies partagées au sein du canal de discussion interne du mouvement, et, de manière marginale, des photographies personnelles produites par l’autrice lors de participation à des sessions, ou transmises directement par des activites connu·es personnellement. Chaque photographie a été documentée et codée manuellement.
Les photographies ne sont pas disponibles dans la base de donnée car leur diffusion n'a pas été autorisée par le mouvement CFP. Seule une diffusion ponctuelle dans le manuscrit de thèse a été autorisée.
Les informations visibles sur l’image (texte du collage, localisation, éléments urbains), les métadonnées associées (date de publication, indications textuelles fournies par les activistes) et les vérifications ultérieures de terrain ou par comparaison visuelle (Google Street View, repérages complémentaires) ont permis de produire un jeu de données structuré. Ce dernier organise l’ensemble des collages parisiens selon un ensemble de variables : date de production, session de collage, localisation, adresse, contenu textuel, thématique, niveau de visibilité, type de message, ainsi que diverses informations contextuelles permettant d’analyser l’activité du mouvement dans l’espace urbain.
description: Temporal: 2019-2024
description: temporal: 2019-2024
DOI: 10.15468/dl.rpp8qn
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((101.553 -1.068818, 101.482725 -1.074384, 101.414179 -1.090945, 101.34905 -1.118094, 101.28894 -1.155162, 101.23533 -1.201237, 101.189538 -1.255185, 101.152694 -1.315678, 101.125703 -1.381227, 101.109231 -1.450218, 101.103685 -1.520953, 101.109202 -1.59169, 101.125648 -1.660688, 101.152618 -1.726247, 101.18945 -1.786753, 101.235236 -1.840715, 101.288851 -1.886804, 101.348974 -1.923885, 101.414124 -1.951044, 101.482696 -1.967612, 101.553 -1.97318, 101.623304 -1.967612, 101.691876 -1.951044, 101.757026 -1.923885, 101.817149 -1.886804, 101.870764 -1.840715, 101.91655 -1.786753, 101.953382 -1.726247, 101.980352 -1.660688, 101.996798 -1.59169, 102.002315 -1.520953, 101.996769 -1.450218, 101.980297 -1.381227, 101.953306 -1.315678, 101.916462 -1.255185, 101.87067 -1.201237, 101.81706 -1.155162, 101.75695 -1.118094, 101.691821 -1.090945, 101.623275 -1.074384, 101.553 -1.068818))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047419-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17900390
title: Dataset of chromatic recurrences for joint walking of a blind mother-child dyad

description: Datasets and scripts corresponding to "Chromatic recurrences applied to joint walking time series of a blind mother-child dyad" manuscript (under review)
DOI: 10.5281/zenodo.17900389
title: Dataset of chromatic recurrences for joint walking of a blind mother-child dyad

description: Datasets and scripts corresponding to "Chromatic recurrences applied to joint walking time series of a blind mother-child dyad" manuscript (under review)
DOI: 10.15468/dl.s436jc
title: Occurrence Download

description: A dataset containing 402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "Geometry POLYGON((-6.25617 41.0851,27.48128 41.0851,27.48128 72.26782,-6.25617 72.26782,-6.25617 41.0851))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Salix bicolor"
 ]
}

 The dataset includes 402 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047420-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15045918
title: GNSS Scintillation data from Finland, Norway, Greenland and Canada for the geomagnetic storm of May 2024

description: The geomagnetic storm of May 2024 was a major space weather event. This dataset includes data from more than 40 groundbased GNSS scintillation receivers throughout the Arctic. The data files contain both a large number of scintillation data parameters and all the metadata needed to make use of the data. The data files are in the HDF5/netCDF4 format, and a format description document explaining the structure of the file contents is included here. At the time of submission the format description, plus additional useful scripts, is also available at: https://github.com/kartverket/BiScEF
DOI: 10.5281/zenodo.15045917
title: GNSS Scintillation data from Finland, Norway, Greenland and Canada for the geomagnetic storm of May 2024

description: The geomagnetic storm of May 2024 was a major space weather event. This dataset includes data from more than 40 groundbased GNSS scintillation receivers throughout the Arctic. The data files contain both a large number of scintillation data parameters and all the metadata needed to make use of the data. The data files are in the HDF5/netCDF4 format, and a format description document explaining the structure of the file contents is included here. At the time of submission the format description, plus additional useful scripts, is also available at: https://github.com/kartverket/BiScEF
DOI: 10.15468/dl.3x846k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((119.433 -1.068818, 119.362725 -1.074384, 119.294179 -1.090945, 119.22905 -1.118094, 119.16894 -1.155162, 119.11533 -1.201237, 119.069538 -1.255185, 119.032694 -1.315678, 119.005703 -1.381227, 118.989231 -1.450218, 118.983685 -1.520953, 118.989202 -1.59169, 119.005648 -1.660688, 119.032618 -1.726247, 119.06945 -1.786753, 119.115236 -1.840715, 119.168851 -1.886804, 119.228974 -1.923885, 119.294124 -1.951044, 119.362696 -1.967612, 119.433 -1.97318, 119.503304 -1.967612, 119.571876 -1.951044, 119.637026 -1.923885, 119.697149 -1.886804, 119.750764 -1.840715, 119.79655 -1.786753, 119.833382 -1.726247, 119.860352 -1.660688, 119.876798 -1.59169, 119.882315 -1.520953, 119.876769 -1.450218, 119.860297 -1.381227, 119.833306 -1.315678, 119.796462 -1.255185, 119.75067 -1.201237, 119.69706 -1.155162, 119.63695 -1.118094, 119.571821 -1.090945, 119.503275 -1.074384, 119.433 -1.068818))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047421-251120083545085/datasets/export for details.
DOI: 10.15468/dl.k5w7js
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((104.81 -6.33912,105.71119 -5.98947,106.54644 -4.98302,108.87636 -2.878,107.40368 -1.01083,105.13971 1.29694,104.43029 1.27647,103.92288 1.18847,103.41029 1.18329,103.10998 1.37482,101.61881 2.35287,100.27885 3.50514,98.7232 4.84313,95.75564 6.84495,94.56861 6.47651,93.6386 5.57272,92.98945 3.72418,97.10694 -3.26374,103.48719 -6.29456,104.81 -6.33912))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Shorea sumatrana"
 ]
}

 The dataset includes 35 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047423-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tw96rv
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microhyla gadjahmadai"
 ]
}

 The dataset includes 16 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047424-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17899626
title: Rp-Bp and the Ribotools box

description: Supplementary information 

This repository contains supplementary data for Rp-Bp and the Ribotools box for translatome profiling.

Description of files



hiPSC-CMs.denovo.slim.gtf A de novo assembled transcriptome annotation for human iPSCs differentiation into cardiomyocytes. Paired-end RNA-seq reads were first trimmedand filtered using Flexbar with the following options `flexbar -n 15 -z GZ -m 30 -u 0  -q TAIL -qt 28 -a adapters.fa -qf sanger -j`. Common contaminantswere removed with Bowtie2 using a built-in index combining mitochondiral and rRNA sequences with  `bowtie2 --no-unal --omit-sec-seq --threads 20 --mm --seed 1337 --time --un-conc-gz`. Remaing reads were mapped using STAR with `STAR --runThreadN 40 --genomeLoad NoSharedMemory --readFilesCommand zcat --outReadsUnmapped Fastx --outSAMattributes NH HI AS nM NM MD jM jI XS --outSJfilterOverhangMin 15 15 15 15 --outFilterMultimapNmax 20 --chimMultimapNmax 20 --outFilterScoreMin 1 --outFilterMatchNminOverLread 0.7 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 15    --alignSJDBoverhangMin 10 --alignSoftClipAtReferenceEnds No --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15 --sjdbGTFfile GRCh38.102.gtf --quantMode GeneCounts --twopassMode Basic --chimOutType Junctions`. Soft clipping was removed and the output SAM file was passed to samtools for compression, sorting and indexing. To reconstruct de novo transcriptomes for each sample, guided by a reference transcriptome annotation (Ensembl release 102), stringtie was used `stringtie -G GRCh38.102.gtf -p 2 -v --rf --conservative`, followed by `stringtie --merge -G GRCh38.102.gtf -p 2 -v`. Finally, the annotations were merged into a non-redundant set of features and compared with the reference annotation using `gffcompare -r  GRCh38.102.gtf -V -R`.

hiPSC-CMs.Ribo-seq-ORFs.bed.gzRibo-seq ORFs predicted and annotated with Rp-Bp with `run-all-rpbp-instances --star-options "--quantMode TranscriptomeSAM GeneCounts" --use-slurm --num-cpus 6 --mem 250G --keep-intermediate-files --merge-replicates --run-replicates` (default options and parameters).  

hiPSC-CMs.Ribo-seq-proteins.slim.fa Translated Ribo-seq ORFs sequences. This file is short of 82 Ribo-seq ORFs that have duplicate protein sequences.

rnaseq-results.zipCount tables (trimmed RNA-seq reads) obtained with Ribotools for both Ribo-seq ORFs and genes.

riboseq-results.zipCount tables (periodic Ribo-seq reads) obtained with Ribotools for both Ribo-seq ORFs and genes.

tea-results.zipTranslation efficiency (TE) analyses obatine with Ribotools using the default LRT method for  both Ribo-seq ORFs and genes for selected contrasts (d1_vs_d0, d5_vs_d0, d5_vs_d1, d7_vs_d5, d17_vs_d5, d17_vs_d7, d31_vs_d17).

adapters.faGeneral list of RNA-seq adapters.

riboseq-adapters.faList of Ribo-seq adapters.
DOI: 10.5281/zenodo.17899627
title: Rp-Bp and the Ribotools box

description: Supplementary information 

This repository contains supplementary data for Rp-Bp and the Ribotools box for translatome profiling.

Description of files



hiPSC-CMs.denovo.slim.gtf A de novo assembled transcriptome annotation for human iPSCs differentiation into cardiomyocytes. Paired-end RNA-seq reads were first trimmedand filtered using Flexbar with the following options `flexbar -n 15 -z GZ -m 30 -u 0  -q TAIL -qt 28 -a adapters.fa -qf sanger -j`. Common contaminantswere removed with Bowtie2 using a built-in index combining mitochondiral and rRNA sequences with  `bowtie2 --no-unal --omit-sec-seq --threads 20 --mm --seed 1337 --time --un-conc-gz`. Remaing reads were mapped using STAR with `STAR --runThreadN 40 --genomeLoad NoSharedMemory --readFilesCommand zcat --outReadsUnmapped Fastx --outSAMattributes NH HI AS nM NM MD jM jI XS --outSJfilterOverhangMin 15 15 15 15 --outFilterMultimapNmax 20 --chimMultimapNmax 20 --outFilterScoreMin 1 --outFilterMatchNminOverLread 0.7 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 15    --alignSJDBoverhangMin 10 --alignSoftClipAtReferenceEnds No --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15 --sjdbGTFfile GRCh38.102.gtf --quantMode GeneCounts --twopassMode Basic --chimOutType Junctions`. Soft clipping was removed and the output SAM file was passed to samtools for compression, sorting and indexing. To reconstruct de novo transcriptomes for each sample, guided by a reference transcriptome annotation (Ensembl release 102), stringtie was used `stringtie -G GRCh38.102.gtf -p 2 -v --rf --conservative`, followed by `stringtie --merge -G GRCh38.102.gtf -p 2 -v`. Finally, the annotations were merged into a non-redundant set of features and compared with the reference annotation using `gffcompare -r  GRCh38.102.gtf -V -R`.

hiPSC-CMs.Ribo-seq-ORFs.bed.gzRibo-seq ORFs predicted and annotated with Rp-Bp with `run-all-rpbp-instances --star-options "--quantMode TranscriptomeSAM GeneCounts" --use-slurm --num-cpus 6 --mem 250G --keep-intermediate-files --merge-replicates --run-replicates` (default options and parameters).  

hiPSC-CMs.Ribo-seq-proteins.slim.fa Translated Ribo-seq ORFs sequences. This file is short of 82 Ribo-seq ORFs that have duplicate protein sequences.

rnaseq-results.zipCount tables (trimmed RNA-seq reads) obtained with Ribotools for both Ribo-seq ORFs and genes.

riboseq-results.zipCount tables (periodic Ribo-seq reads) obtained with Ribotools for both Ribo-seq ORFs and genes.

tea-results.zipTranslation efficiency (TE) analyses obatine with Ribotools using the default LRT method for  both Ribo-seq ORFs and genes for selected contrasts (d1_vs_d0, d5_vs_d0, d5_vs_d1, d7_vs_d5, d17_vs_d5, d17_vs_d7, d31_vs_d17).

adapters.faGeneral list of RNA-seq adapters.

riboseq-adapters.faList of Ribo-seq adapters.
DOI: 10.15468/dl.xu8vdx
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((103.664 -1.056818, 103.593725 -1.062384, 103.52518 -1.078945, 103.460051 -1.106094, 103.399941 -1.143162, 103.346331 -1.189237, 103.30054 -1.243185, 103.263696 -1.303678, 103.236705 -1.369227, 103.220233 -1.438218, 103.214688 -1.508953, 103.220205 -1.579691, 103.23665 -1.648688, 103.26362 -1.714247, 103.300452 -1.774753, 103.346238 -1.828715, 103.399853 -1.874804, 103.459976 -1.911885, 103.525125 -1.939044, 103.593696 -1.955612, 103.664 -1.961181, 103.734304 -1.955612, 103.802875 -1.939044, 103.868024 -1.911885, 103.928147 -1.874804, 103.981762 -1.828715, 104.027548 -1.774753, 104.06438 -1.714247, 104.09135 -1.648688, 104.107795 -1.579691, 104.113312 -1.508953, 104.107767 -1.438218, 104.091295 -1.369227, 104.064304 -1.303678, 104.02746 -1.243185, 103.981669 -1.189237, 103.928059 -1.143162, 103.867949 -1.106094, 103.80282 -1.078945, 103.734275 -1.062384, 103.664 -1.056818))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 55 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047425-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wzcj5g
title: Occurrence Download

description: A dataset containing 442892 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Netherlands",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Haematopus ostralegus",
 "Year 2000-2024"
 ]
}

 The dataset includes 442892 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047374-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48320/ea581d81-f122-4de2-86f8-e679729623fa
title: Opinions and Views of the Population of Ukraine: May 2025 (KIIS Omnibus 2025/05)
DOI: 10.5281/zenodo.17901056
title: Opinions and Views of the Population of Ukraine: May 2025 (KIIS Omnibus 2025/05) – Data from a nationwide public opinion poll conducted by KIIS in May 2025

description: "Opinions and Views of the Population of Ukraine" is a regular omnibus survey, conducted by Kyiv International Institute of Sociology (KIIS) among Ukraine's adult population and covering a wide range of topics. The data presented here is a subset of the survey conducted in May 2025 and includes KIIS's own research questions.
The survey addresses the following issues: 
•	readiness for territorial concessions for peace; 
•	how long Ukrainians are ready to bear the burden of war; 
•	trust in Volodymyr Zelenskyy; 
•	perceptions of the policies of Europe and the United States toward Ukraine in the context of the ongoing Russo-Ukrainian war;
•	attitudes toward the United States, its people, its leadership, and Trump's presidency; 
•	perceptions of Russia's resilience; 
•	perceptions of Ukraine's future in 10 years; 
•	Ukraine's progress toward becoming a unified political nation. 
Data collection took place from 15 May to 3 June 2025.
The full sample included 2,004 respondents, divided into subsamples (~1,000 respondents) for different question groups.
The data is available in an SAV format (Ukrainian, English) and a converted CSV format (with a codebook).
The Data Documentation includes a short overview and discussion of survey results (with frequency tables in Annex 1) as well as the relevant parts of the original questionnaire in Ukrainian (Annex 2).
description: Published on Discuss Data, https://discuss-data.net/dataset/ea581d81-f122-4de2-86f8-e679729623fa/
description: Method(s) of data collection: Public Opinion Poll