cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21954/ou.rd.30374830.v2
title: SoFAIR Project Dataset - An annotated dataset of software mentions in full text scientific articles.

description: This is a multidisciplinary dataset of research papers, annotated with software mentions, built by the SoFAIR project in collaboration with the CLARIN-PL team. The SoFAIR project aims to support the reproducibility of research and the reuse of data and to recognise the contribution of software developers. The dataset was created through a workflow consisting of text selection, automatic pre-annotation of documents using the Softcite software-mentions tool and manual gold standard annotation. The dataset contains more than 9,000 software mentions, divided into 10 categories, as well as more than 2,000 relationships between mentions, which come from almost 500 texts belonging to 18 scientific disciplines. The dataset presented here contains detailed data and statistics that can be used to evaluate language models or to further develop software extraction tools. The dataset is available in TEI XML format and has been made available under a CC-BY license.This dataset was created as part of the project "Making Software FAIR: A machine-assisted workflow for the research software lifecycle”, under the program CHIST-ERA Open & Re-usable Research Data & Software (CHIST-ERA-22-ORD-08). <br>
DOI: 10.21954/ou.rd.30374830.v1
title: SoFAIR Project Dataset - An annotated dataset of software mentions in full text scientific articles.

description: This is a multidisciplinary dataset of research papers, annotated with software mentions, built by the SoFAIR project in collaboration with the CLARIN-PL team. The SoFAIR project aims to support the reproducibility of research and the reuse of data and to recognise the contribution of software developers. The dataset was created through a workflow consisting of text selection, automatic pre-annotation of documents using the Softcite software-mentions tool and manual gold standard annotation. The dataset contains more than 9,000 software mentions, divided into 10 categories, as well as more than 2,000 relationships between mentions, which come from almost 500 texts belonging to 18 scientific disciplines. The dataset presented here contains detailed data and statistics that can be used to evaluate language models or to further develop software extraction tools. The dataset is available in TEI XML format and has been made available under a CC-BY license.
DOI: 10.15468/dl.hq5vmd
title: Occurrence Download

description: A dataset containing 5915 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Andrena wilkella",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5915 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038907-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6dxta
title: Occurrence Download

description: A dataset containing 21010 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungi - Herbarium of The National Natural History Collections"
 ]
}

 The dataset includes 21010 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038908-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17177547
title: MSc Thesis Genome Annotation Data for non-Saccharomyces yeast and microalgal species

description: This repository contains data from my MSc thesis in Bioinformatics and Computational Biology: “Improving the genome annotations of non-Saccharomyces yeast and microalgal species.”

The study focuses on generating high-quality genome annotations for:

Torulaspora delbrueckii LO544

Lachancea thermotolerans IWBT Y1240

Chlorella sorokiniana

These species, with wine-related origins, play important roles in wine fermentation and winery wastewater biotechnology. Despite the availability of genomic data, recent annotation data for these strains is lacking, limiting the exploitation of other omics datasets and their biotechnological potential. This work aimed to address that gap by producing improved genome annotations. The bioinformatics pipeline in this study assembles transcriptomes, evaluates sequencing data quality, and performs structural and functional annotation using MAKER and eggNOG-mapper. It also validates the improved annotations via differential gene expression and functional enrichment to assess biological relevance.

Contents

Structural Annotations (MAKER):

Final consensus GFF3 files

Evidence alignments

Combined evidence + annotation files

BUSCO scores and genome annotation statistics

Functional Annotations (eggNOG-mapper):

XLSX reports with predicted protein names, PFAM domains, GO terms, KEGG pathways and modules, and COG functional categories

Validation Analysis (only tested on the Torulaspora delbrueckii strain):

Differential gene expression (DESeq2 results)

DEG visualizations

GO and KEGG enrichment graphs

Significance

These resources provide a foundation for future experimental and bioinformatics research aimed at leveraging the biotechnological applications of non-Saccharomyces yeasts and microalgal species.
DOI: 10.5281/zenodo.17623355
title: MSc Thesis Genome Annotation Data for non-Saccharomyces yeast and microalgal species

description: This repository contains data from my MSc thesis in Bioinformatics and Computational Biology: “Improving the genome annotations of non-Saccharomyces yeast and microalgal species.”

The study focuses on generating high-quality genome annotations for:

Torulaspora delbrueckii LO544

Lachancea thermotolerans IWBT Y1240

Chlorella sorokiniana

These species, with wine-related origins, play important roles in wine fermentation and winery wastewater biotechnology. Despite the availability of genomic data, recent annotation data for these strains is lacking, limiting the exploitation of other omics datasets and their biotechnological potential. This work aimed to address that gap by producing improved genome annotations. The bioinformatics pipeline in this study assembles transcriptomes, evaluates sequencing data quality, and performs structural and functional annotation using MAKER and eggNOG-mapper. It also validates the improved annotations via differential gene expression and functional enrichment to assess biological relevance.

Contents

Structural Annotations (MAKER):

Final consensus GFF3 files

Evidence alignments

Combined evidence + annotation files

BUSCO scores and genome annotation statistics

Functional Annotations (eggNOG-mapper):

XLSX reports with predicted protein names, PFAM domains, GO terms, KEGG pathways and modules, and COG functional categories

Validation Analysis (only tested on the Torulaspora delbrueckii strain):

Differential gene expression (DESeq2 results)

DEG visualizations

GO and KEGG enrichment graphs

Significance

These resources provide a foundation for future experimental and bioinformatics research aimed at leveraging the biotechnological applications of non-Saccharomyces yeasts and microalgal species.
DOI: 10.6084/m9.figshare.30636665
title: PMF-NEChina-40D: dynamic maps of plastic-mulched farmlands in Northeast China from 1985 to 2025

description: We provide PMF-NEChina-40D, the first plastic-mulched farmlands (PMFs) dynamic monitoring dataset in Northeast (NE) China for the past four decades from 1985 to 2025. Multi-sensor Landsat series and Sentinel-2 imagery were processed on the Google Earth Engine platform, and a dual-temporal PMFs mapping framework integrating film-on and film-off stages was proposed. Specifically, the Random Forest classifier, combined with grid-based partitioned modeling, was used to produce PMFs maps for nine time steps and every five years, including 1985, 1990, 1995, 2000, 2005, 2010, 2015, 2020 and 2025. Training and validation samples were generated through visual interpretation supported by multi-source satellite imageries and field surveys. Classification accuracy was evaluated using multiple metrics, with average user’s accuracy, producer’s accuracy, F1 score and overall accuracy exceeding 90%. The resulting dataset, PMF-NEChina-40D, yields the first long time-series PMFs distribution maps of Northeast China with high spatial resolution across the past four decades. The dataset offers a reusable resource for studies of agricultural land management, environmental assessment and sustainable development in Northeast China black soil region, and can support applications in other regions with similar agricultural practices.
DOI: 10.6084/m9.figshare.30636665.v1
title: PMF-NEChina-40D: dynamic maps of plastic-mulched farmlands in Northeast China from 1985 to 2025

description: We provide PMF-NEChina-40D, the first plastic-mulched farmlands (PMFs) dynamic monitoring dataset in Northeast (NE) China for the past four decades from 1985 to 2025. Multi-sensor Landsat series and Sentinel-2 imagery were processed on the Google Earth Engine platform, and a dual-temporal PMFs mapping framework integrating film-on and film-off stages was proposed. Specifically, the Random Forest classifier, combined with grid-based partitioned modeling, was used to produce PMFs maps for nine time steps and every five years, including 1985, 1990, 1995, 2000, 2005, 2010, 2015, 2020 and 2025. Training and validation samples were generated through visual interpretation supported by multi-source satellite imageries and field surveys. Classification accuracy was evaluated using multiple metrics, with average user’s accuracy, producer’s accuracy, F1 score and overall accuracy exceeding 90%. The resulting dataset, PMF-NEChina-40D, yields the first long time-series PMFs distribution maps of Northeast China with high spatial resolution across the past four decades. The dataset offers a reusable resource for studies of agricultural land management, environmental assessment and sustainable development in Northeast China black soil region, and can support applications in other regions with similar agricultural practices.
DOI: 10.48623/aperta.286406
title: Overcoming Acquired 5-Fu Resistance In Gastric Cancer: Oleuropein Targets Proliferation, Migration And Survival Pathways

description: 5-Fluorouracil (5-FU) remains a cornerstone in gastric cancer (GC) treatment; however, chemoresistance limits its efficacy. Oleuropein (OL), a phenolic compound in olive leaf extract, has emerged as a low-toxicity candidate with antitumor-potential. A 5-FU-resistant AGS subline (AGS-FUR) was established via stepwise drug exposure. The effects of OL-only or in combination with 5-FU, on proliferation (xCELLigence), apoptosis (Annexin V/PI), ROS, colony formation, migration, and EMT/CSC gene expression and proteomic analyses were assessed in AGS and AGS-FUR cells. OL exhibited dose- and time-dependent anti-proliferative effects, with IC50 values of 73.86µM in AGS cells and 94.58µM in AGS-FUR cells (p&lt;0.0001). Combination therapy showed additive efficacy, significantly increasing apoptosis (p&lt;0.0001) and partially reversing resistance-associated survival. Notably, OL reduced ROS even in AGS-FUR cells but retained proapoptotic effects, suggesting a redox-independent mechanism. In resistant cells unresponsive to 5-FU, combined treatment suppressed colony formation 22.2-fold (p&lt;0.0001). OL also downregulated the CSC markers <em>CD133</em> and <em>NANOG </em>(p&lt;0.05) and inhibited migration/EMT by reducing wound closure and repressing the effects of 5-FU alone on the expression of <em>CDH2</em> (22.2-fold; p&lt;0.0001) and <em>ZEB1</em> (3.83-fold; p&lt;0.05). Proteomic profiling identified 3.392 proteins, of which 232 were highly confidently differentially expressed. Resistance is associated with alterations in chromosome organization, mitochondrial function, and RNA processing. Strikingly, OL suppressed protein levels in AGS cells but upregulated them in AGS-FUR cells, indicating opposing cell line-specific regulation. Overall, OL enhances 5-FU efficacy by impairing proliferation, stemness, and invasion while modulating EMT and apoptosis, underscoring its potential as an adjuvant for overcoming GC chemoresistance.
DOI: 10.15468/dl.avmty9
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriocaulago",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038910-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7ve4x
title: Occurrence Download

description: A dataset containing 4853 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Andrena ovatula",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4853 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038911-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57903/uj/wtmvks
title: The elasticity of liposomes has no effect on their in vivo behavior - replication data

description: Data generated during studies concerning in vivo characteristics of liposomes modified with silicone layer.
DOI: 10.15468/dl.t2655p
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ahmadiago",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038913-251025141854904/datasets/export for details.
DOI: 10.15468/dl.z7rymj
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Andrena hypopolia",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "HasCoordinate is true"
 ]
}

 The dataset includes 82 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038912-251025141854904/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.30636728
title: <b>Figures and Datasets for manuscript SLM YOLO Light Dual Domain Data Augmentation and Lightweight Architecture for Robust Powder Bed Defect Detection</b>

description: The shared materials include:<br>(1) the original powder-bed images used in this study,<br>(2) the complete set of training hyperparameters for all experiments, and<br>(3) the recorded loss values from the model training process.
DOI: 10.6084/m9.figshare.30636728.v1
title: <b>Figures and Datasets for manuscript SLM YOLO Light Dual Domain Data Augmentation and Lightweight Architecture for Robust Powder Bed Defect Detection</b>

description: The shared materials include:<br>(1) the original powder-bed images used in this study,<br>(2) the complete set of training hyperparameters for all experiments, and<br>(3) the recorded loss values from the model training process.
DOI: 10.5281/zenodo.17582770
title: Semi-structured interviews with linguists about Open Science

description: This dataset contains the anonymised transcripts of 26 semi-structured interviews conducted with linguistics students and researchers between late February and early April 2025. The interviews were conducted by Elen Le Foll via Zoom and last around half-an-hour (range: 13–52 min). All were conducted in English except one (A01 in German).

They were first transcribed using a local installation of Whisper (Radford et al. 2022). The automatic transcriptions were subsequently manually checked, corrected, and anonymised by two student research assistants, Vishar Kavehamoli and Julia Weinberger, and Elen Le Foll. 

The coding was performed by Elen Le Foll using OpenQDA (Belli et al. 2025). The CSV file contains all the coded passages and their corresponding categories, as exported from OpenQDA. Note that passages may be listed several times, if they were assigned several codes.For further details, please refer to the README file.
DOI: 10.5281/zenodo.17630137
title: Semi-structured interviews with linguists about Open Science

description: This dataset contains the anonymised transcripts of 26 semi-structured interviews conducted with linguistics students and researchers between late February and early April 2025. The interviews were conducted by Elen Le Foll via Zoom and last around half-an-hour (range: 13–52 min). All were conducted in English except one (A01 in German).

They were first transcribed using a local installation of Whisper (Radford et al. 2022). The automatic transcriptions were subsequently manually checked, corrected, and anonymised by two student research assistants, Vishar Kavehamoli and Julia Weinberger, and Elen Le Foll. 

The coding was performed by Elen Le Foll using OpenQDA (Belli et al. 2025). The CSV file contains all the coded passages and their corresponding categories, as exported from OpenQDA. Note that passages may be listed several times, if they were assigned several codes.For further details, please refer to the README file.
DOI: 10.5518/1459
title: plos_one_carehome_SNA.xls

description: Social network data from four UK care homes with and without nursing. Dates of data collection range from Feb 2021 to Jun 2022. Dataset has two sheets. Sheet one (combined_edges) contains relationships and sheet two (combined_nodes) contains ID (person and home) and community role (staff, resident) and Social network statistics/measures (degree, clustering coefficient, triangles, modularity and weighted degree.)
DOI: 10.15468/dl.96abpa
title: Occurrence Download

description: A dataset containing 3287 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.14031 46.1502,13.86684 46.1502,13.86684 48.09349,10.14031 48.09349,10.14031 46.1502))",
 "HasCoordinate is true",
 "TaxonKey is Sesiidae"
 ]
}

 The dataset includes 3287 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038916-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hp6wzg
title: Occurrence Download

description: A dataset containing 225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Andrena orbitalis",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "HasCoordinate is true"
 ]
}

 The dataset includes 225 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038918-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jewur
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Yelsemia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 13 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038919-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a99ptq
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Platypodiella spectabilis"
 ]
}

 The dataset includes 146 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038921-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34810/data1988
title: Base de dades bibliogràfica de l'Arxiu Digital Sebastià Juan Arbó

description: Aquest conjunt de dades presenta en format JSON la base de dades bibliogràfica integrada en l'Arxiu Digital Sebastià Juan Arbó. Aquestes dades són també la base per a la creació d'un llibre electrònic titulat «Bibliografia completa de Sebastià Juan Arbó (1918-2025)». La publicació d’aquesta obra, que tindrà lloc l’any 2026, respon a la necessitat de recuperar el llegat d'un escriptor essencial per entendre la literatura catalana i espanyola del segle XX, documentant tant la seva producció com els materials generats al voltant de la seva figura. Presentem aquí, en format JSON, el conjunt de dades que conformen cadascun dels apartats del volum, els quals també formen part d’una base de dades integrada en l'Arxiu Digital Sebastià Juan Arbó, un projecte en desenvolupament.
DOI: 10.15468/dl.bsxjfr
title: Occurrence Download

description: A dataset containing 58851 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is August",
 "OccurrenceStatus is Present",
 "TaxonKey is Erinaceus europaeus",
 "Year 2025-2025"
 ]
}

 The dataset includes 58851 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038895-251025141854904/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.30636767
title: <b>Mapeamento da Presença Digital de Periódicos de Acesso Aberto em Ciência da Informação: Uma Análise das Redes Sociais</b>

description: Este conjunto de dados refere-se à coleta de dados realizada para o Trabalho de Conclusão de Curso (TCC) intitulado "Mapeamento da Presença Digital de Periódicos de Acesso Aberto em Ciência da Informação: Uma Análise das Redes Sociais". O objetivo da pesquisa foi mapear a presença institucional de periódicos científicos da área de Ciência da Informação (CI), que adotam o modelo de Acesso Aberto, nas cinco principais redes sociais digitais (Facebook, Instagram, X, LinkedIn e YouTube).Metodologia de Coleta<br><b>Seleção da Amostra:</b> O universo da pesquisa foi extraído do <b>Directory of Open Access Journals (DOAJ)</b> em 2025, utilizando o filtro de busca "Information Science".<b>Coleta (Periódicos):</b> Foram identificados <b>137 periódicos</b> de Acesso Aberto da área de Ciência da Informação.<b>Coleta (Redes Sociais):</b> Foi realizada uma verificação (via plataforma Altmetrics.com e busca direta) para identificar quais dos 137 periódicos possuíam perfis oficiais ativos nas cinco redes sociais analisadas.Conteúdo dos DadosOs arquivos anexos contêm o conjunto de dados brutos e tratados utilizados para gerar os resultados da pesquisa, incluindo:A lista mestra dos <b>137 periódicos</b> de CI em Acesso Aberto identificados no DOAJ.A distribuição geográfica (país de origem) de cada um dos 137 periódicos.O mapeamento detalhado indicando quais dos <b>52 periódicos</b> identificados possuem presença digital.A lista de periódicos que <b>não possuem</b> presença ativa nas redes analisadas.Tabelas de frequência que quantificam a adesão total por plataforma (ex: total de periódicos no Facebook, total no Instagram, etc.).