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Dataset results
191 results for “open research”
Cayla et al., 2020, Wellcome Open Research - Underlying data
<p>Underlying dataset for the identifications of low-complexity regions (LCRs) in the proteome of Trypanosoma brucei.</p> <p>- Supplement File 2.xlsx (Position of every InterPro domain and LCR identified. All genes are provided with indication on chromosome localisation, presence of transmembrane domains, signal peptides and the localisation of the encoded proteins, either predicted using DeepLoc<sup>37</sup> or observed (Tryptag<sup>38</sup>)).</p> <p>- Supplement File 3.xlsx (List of genes and Molecular Function gene ontology (GO) enrichment analysis of proteins with predicted LCRs in the N-terminal, central part or C-terminal or the different possible combinations.)</p> <p>- Supplement File 4.xlsx (Property analysis of sequences of every InterPro and LCRs identified.)</p> <p>- Supplement File 5.xlsx (List of genes and Molecular GO enrichment analysis of proteins presenting a Low (<8) or High (>9) polarity index level.)</p> <p>- Supplement File 6.xlsx (List and position of PTMs present on InterPro domains and LCRs. The different datasets from which the PTMs have been extracted can be found in the Zhang2020, Benz2019, Cayla2019, Urbaniak2013, Ooi2020, Fisk2012, Lott2012 and Moretti2017<sup>12,13,15,17–19,27,28</sup> columns. The sequence properties of the domains/LCRs on which these PTMs are located are also indicated. The list of modifications identified in Ooi <em>et al.</em> 2020<sup>28</sup> present on LCRs are indicated in the second sheet.)</p> <p>- Supplement File 7.xlsx (List and position of LCRs, signal peptides and their overlap.)</p>
Global Naturalized Alien Flora (GloNAF). Open access data to support research on understanding global plant invasions.
<p>This dataset is a snapshot of the Global Naturalized Alien Flora (GloNAF) database, version 2.02. GloNAF is a continuously updated, curated compilation of alien naturalized vascular plant inventories for geographic regions from around the world. The dataset has 16,429 unique taxa reported as naturalized or invasive and covers 1,343 regions (including 427 islands) from 336 data sources. For each region, the status (invasive, naturalized) is provided as listed in the original source. We provide the scientific names included with the original data source, and the matching accepted name or synonym of the taxon as given in the World Checklist of Vascular Plants (WCVP) Version 12. In addition, we provide an ESRI shapefile of polygons for each region. We also provide several variables that can be used to filter the data according to quality and completeness of alien taxon lists, which vary among the combinations of regions and data sources.</p> <p>The 'glonaf_flora2.csv' file lists the IDs ('taxon_wcvp_id') of all naturalized taxa contained in GloNAF and the regions they occur in. The 'glonaf_taxon_wcvp.csv' lists the original taxon names provided in the source data along with the corresponding accepted taxon name from the WCVP (version 12) for all alien taxa in GloNAF, regardless of their naturalization status. To link taxon names with naturalization records, join the 'id' column of the 'glonaf_taxon_wcvp.csv' file to the 'taxon_wcvp_id' column in 'glonaf_flora2.csv' . Additional information regarding the original source of the data ('glonaf_reference.csv'), specific attributes of the taxon lists ('glonaf_list.csv') and the region ('glonaf_region.csv') can also be joined similarly to 'glonaf_flora2.csv '. </p> <p> </p>
Open Research Skills Workshops - Open access publishing Workshop
<p><strong>This is the first workshop on Open Access Publishing in a series of workshops about Open Research Skills.</strong></p><p>This workshop covers:</p><p>Introduction to open access publishing</p><ul><li>Types of open access publishing</li><li>Examples of open access publishing journals and platforms</li><li>Benefits of open access publishing</li><li>Types of outputs that can be published</li></ul><p>Demonstration </p><ul><li>Demonstrating open publishing </li><li>Showing how a reproducible article is published and all the different outputs that are linked to it and how to do this</li></ul><p>Exercise</p><ul><li>Discuss and explore open publishing giving examples of different articles that show how open publishing works. We will pick those that show data and code deposited in repositories and also that use of protocol.io for publishing open methods</li></ul><p><strong>List of training workshops in Open Research Skills:</strong></p><ul><li><strong>24th February 2023 - Open access publishing</strong></li><li>24th March 2023 - Using repositories</li><li>21st April 2023 - GitHub basics</li><li>28th April 2023 - GitHub collaborative workflows</li><li>26th May 2023 - Standard vocabularies and ontologies</li><li>30th June 2023 - FAIR data</li></ul><p><strong>Project overview:</strong></p><p>Our project aims to upskill participants in open research skills to increase the quality and reusability of phytolith research and related disciplines such as archaeology, palaeosciences and plant sciences. We will run six hands-on training workshops on open access publishing and research outputs, using repositories, ontologies and standard vocabularies, implementation of FAIR Guidelines for phytolith research, and two workshops on Github basic and advanced skills. The materials from all workshops will be archived as self-study courses on our website (<a href="https://open-phytoliths.netlify.app/">https://open-phytoliths.netlify.app/</a>). We will also provide translation during workshops and training materials into multiple languages.</p>
Open Access in developing countries – attitudes and experiences of researchers Dataset
<p>A survey was conducted of 507 researchers from the developing world and connected to INASP’s AuthorAID project to ascertain experiences and attitudes to Open Access publishing. This file is the raw output from the survey, with names and email addresses removed to preserve anonymity. </p>
EMB3Rs Open digital research data
<p>The EMB3Rs Unified Modelling Platform is a tool to assist on modelling the recovery of excess heat and its reuse to meet final energy demand within and beyond the boundaries of industrial sites. The tool consists of a knowledge base and several simulation modules.<br> This database comprises the research data generated in the course of the EMB3Rs project by using the EMB3Rs platform.<br> The pdf file contains the detailed description of the database content</p> <p>It has been deposited at Zenodo’s open data repository with DOI 10.5281/zenodo.7994255.</p>
The Hearpiece database of individual transfer functions of an openly available in-the-ear earpiece for hearing device research
<p>We present a database of acoustic transfer functions of the Hearpiece, an openly available multi-microphone multi-driver in-the-ear earpiece for hearing device research. The database includes HRTFs for 87 incidence directions as well as responses of the drivers, all measured at the four microphones of the Hearpiece as well as the eardrum in the occluded and open ear. The transfer functions were measured in both ears of 25 human subjects and a KEMAR with anthropometric ears for five reinsertions of the device. We describe the measurements of the database and analyse derived acoustic parameters of the device. All regarded transfer functions are subject to differences between subjects as well as variations due to reinsertion into the same ear. Also, the results show that KEMAR measurements represent a median human ear well for all assessed transfer functions. The database is a rich basis for development, evaluation and robustness analysis of multiple hearing device algorithms and applications.</p>
Research Data of the 2014 Census of Open Access Repositories in Germany, Austria and Switzerland
<p>The "2014 Census of Open Access Repositories in Germany, Austria and Switzerland” (2014 Census) is a study on the green open access landscape conducted in the course of a project seminar at the Berlin School of Library and Information Science (BSLIS) at Humboldt-Universität zu Berlin. The 2014 Census not only succeeds the "2012 Census of Open Access Repositories in Germany"[1] but enhances it by adding an online survey to the qualitative analysis of the open access repository websites and the automatic validation of its metadata. Like in 2012 the 2014 Census gives insights into the development of open access repositories and current trends in repository design being of substantial use to open access repository operators.</p> <p>This 2014 Census data set represents the data collected in three different ways:</p> <ul> <li>qualitative analysis of the open access repository websites</li> <li>automatic validation of the metadata via OAI-PMH using the DINI-Validator [2] </li> <li>online survey of repository operators</li> </ul> <p>As in 2012 [3] the data set is provided in XLSX as well as in CSV format. The columns represent the criteria and the rows represent the analyzed open access repositories. In the XLSX file the header row gives the definition of each criterion in English and German. In the CSV "content" file the header row is in English short terms. The respective English and German definition can be found in the CSV "readme" file.</p> <p> </p> <p>[1] Vierkant, P. (2013). 2012 Census of Open Access Repositories in Germany: Turning Perceived Knowledge Into Sound Understanding. <em>D-Lib Magazine</em>, 19. http://dx.doi.org/10.1045/november2013-vierkant </p> <p>[2] http://oanet.cms.hu-berlin.de/validator/pages/validation_dini.xhtml</p> <p>[3] Vierkant, Paul; Voigt, Michaela; Dupski, Jens; David, Sammy; Lösch, Mathias (2013): 2012 Census of Open Access Repositories in Germany. fig<strong>share</strong>. <br /> http://dx.doi.org/10.6084/m9.figshare.677099</p>
National Open Access Monitor, Ireland - Research product metadata
<p>This dataset contains the foundational data for the National Open Access Monitor under an open license. OpenAIRE will routinely provide monthly data dumps to Zenodo, encompassing a comprehensive set of data and indicators related to the Open Access Monitor. This collaborative effort ensures accessibility and openness in sharing the data, promoting transparency and facilitating its use for research and analysis purposes.<br>The dataset comprises of the metadata of the research products metadata stored in the parquet format. The file contains two columns ("id", "xml"), the first of which is the OpenAIRE identifier of the research product and the the second the xml representation of the metadata. The schema of the metadata can be found in https://www.openaire.eu/schema/1.0/oaf-1.0.xsd and a detailed description of the contents can be found in https://graph.openaire.eu/docs/ and https://zenodo.org/records/2643199</p>
Open Research Skills Workshops - GitHub basics
<p>This is the third workshop on GitHub basics<strong> </strong>in a series of workshop about Open Research Skills.</p><p>This workshop covers:</p><p><strong>-</strong> Introduction to Github and its uses</p><p>- Demonstration on using GitHub <strong> </strong></p><p>- Basic repo set up and editing</p><p><strong>List of training workshops in Open Research Skills:</strong></p><ul><li>24th February 2023 - Open access publishing</li><li>24th March 2023 - Using repositories</li><li><strong>21st April 2023 - GitHub basics</strong></li><li>28th April 2023 - GitHub collaborative workflows</li><li>26th May 2023 - Standard vocabularies and ontologies</li><li>30th June 2023 - FAIR data</li></ul><p><strong>Project overview:</strong></p><p>Our project aims to upskill participants in open research skills to increase the quality and reusability of phytolith research and related disciplines such as archaeology, palaeosciences and plant sciences. We will run six hands-on training workshops on open access publishing and research outputs, using repositories, ontologies and standard vocabularies, implementation of FAIR Guidelines for phytolith research, and two workshops on Github basic and advanced skills. The materials from all workshops will be archived as self-study courses on our website (<a href="https://open-phytoliths.netlify.app/">https://open-phytoliths.netlify.app/</a>). We will also provide translation during workshops and training materials into multiple languages. </p><p>This video is a basic course in Github. Github is a tool that is used for research project management and history tracking of your work during projects. It can be used to store and collaborate during projects with data, code and documentation. It covers the basic web interface of Github and how to make repositories, add files and folders. It will also include some examples of uses of Github.</p>
Open Research Skills Workshops - GitHub collaborative workflows
<p>This is the fourth workshop on GitHub collaborative workflows in a series of workshop about Open Research Skills.</p><p>This workshop covers:</p><p>- Introduction to version control</p><p>- How to fork a repository</p><p>- Forking exercises</p><p>- How to work in a team and create and merge branches</p><p>- Branching exercises</p><p><strong>List of training workshops in Open Research Skills:</strong></p><ul><li>24th February 2023 - Open access publishing</li><li>24th March 2023 - Using repositories</li><li>21st April 2023 - GitHub basics</li><li><strong>28th April 2023 - GitHub collaborative workflows</strong></li><li>26th May 2023 - Standard vocabularies and ontologies</li><li>30th June 2023 - FAIR data</li></ul><p><strong>Project overview:</strong></p><p>Our project aims to upskill participants in open research skills to increase the quality and reusability of phytolith research and related disciplines such as archaeology, palaeosciences and plant sciences. We will run six hands-on training workshops on open access publishing and research outputs, using repositories, ontologies and standard vocabularies, implementation of FAIR Guidelines for phytolith research, and two workshops on Github basic and advanced skills. The materials from all workshops will be archived as self-study courses on our website (<a href="https://open-phytoliths.netlify.app/">https://open-phytoliths.netlify.app/</a>). We will also provide translation during workshops and training materials into multiple languages. </p><p>Github is a collaborative, project management tool used to run reproducible research projects with version control. In these videos, you will learn how to use version control, how to branch and fork a repository, how to pull a request and how to collaborate as part of a team on GitHub.</p>
Data for publication "Benefits of open access to researchers from lower-income countries: A global analysis of reference patterns in 1980–2020"
<p>Data to reproduce figures for the publication "Benefits of open access to researchers from lower-income countries: A global analysis of reference patterns in 1980–2020" (DOI: 10.1177/01655515241245952). Each file contains the data underlying the figure corresponding to the file name.</p>
The open D1NAMO dataset: A multi-modal dataset for research on non-invasive type 1 diabetes management
<p>The description of the dataset is available at <a href="https://doi.org/10.1016/j.imu.2018.09.003">https://doi.org/10.1016/j.imu.2018.09.003</a></p> <p>The usage of wearable devices has gained popularity in the latest years, especially for health-care and well being. Recently there has been an increasing interest in using these devices to improve the management of chronic diseases such as diabetes. The quality of data acquired through <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/wearable-sensor">wearable sensors</a> is generally lower than what medical-grade devices provide, and existing datasets have mainly been acquired in highly controlled clinical conditions. In the context of the <em>D1NAMO</em> project — aiming to detect <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/glycemic">glycemic</a> events through non-invasive <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/ecg-abnormality">ECG pattern</a> analysis — we elaborated a dataset that can be used to help developing health-care systems based on wearable devices in non-clinical conditions. This paper describes this dataset, which was acquired on 20 healthy subjects and 9 patients with type-1 diabetes. The acquisition has been made in real-life conditions with the <em>Zephyr BioHarness 3</em> wearable device. The dataset consists of <em>ECG</em>, <em>breathing</em>, and <em><a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/accelerometer">accelerometer</a></em> signals, as well as <em>glucose</em> measurements and annotated <em>food pictures</em>. We open this dataset to the scientific community in order to allow the development and evaluation of diabetes management algorithms.</p>
Evaluation Set - Contributions Similarity in the Open Research Knowledge Graph
<p>This evaluation set has been created for evaluating a content-based recommender system in the context of the Open Research Knowledge Graph (ORKG). The recommender system accepts structured ORKG contribution as input and recommends existing contributions in the ORKG semantically relevant to the given one.</p> <p> </p> <p>The evaluation set is manually annotated based on the <a href="https://www.orkg.org/orkg/featured-comparisons">featured comparisons</a> in the ORKG. In the course of this, it has been distinguished between homogeneous (those who are dissimilar in 2-3 properties) and heterogeneous (otherwise) instances. Multiple annotations have been obtained for the former and exactly one for the latter.</p> <p> </p> <p>It has been also distinguished between "with_response" and "without_response" instances (50 instances for each). The former are those contributions for them the initial version of the contributions similarity service has found similarities and the latter are the opposite case.</p> <p> </p> <p>This evaluation set has been created and applied on a modified version of the contributions similarity service in the context of <a href="https://doi.org/10.15488/11834">this master's thesis</a>. The modified version of the service has simplified the document representation of contributions that are stored in an ElasticSearch index by omitting redundant terms.</p> <p>The evaluation set has the following schema:</p> <pre><code class="language-json">{ "with_response": [ { "contribution_id": "some_id", "comparison_id": "some_id", "comparison_label": "some_label", "contribution_label": "some_label", "paper": "some_id", "research_field": "some_id", "research_problems": [ "some_id" ], "annotations": [ "some_id of a similar contribution", ... ] }, ... ], "without_response": [ ... ] }</code></pre> <p> </p>
Open Science and Authorship of Supplementary Material for the MES research community
<p>This spreadsheet contains the data and the results from the analysis described in the paper "Open Science and Authorship of Supplementary Material. Evidence from a Research Community." being accepted at STI 2022.</p>
Monitoring open access publishing of NWO funded research (2015-2021) data set
<p>This is the dataset underlying the report "Monitoring open access publishing of NWO funded research" (<a href="https://doi.org/10.5281/zenodo.7041897">https://doi.org/10.5281/zenodo.7041897</a>)</p> <p>The report presents statistics on the extent to which publications from the period 2015–2021 funded by NWO are available in Open Access. The analyses presented in this report also cover publications funded by the Netherlands Organisation for Health Research and Development ZonMw. This report builds on two earlier reports, published in <a href="https://zenodo.org/record/4446042">2020</a> and <a href="https://zenodo.org/record/5056043">2021</a>, covering publications from the period 2015–2018 and 2015-2020, respectively.</p>
Coverage and quality of open metadata for Dutch research output - dataset
<p>Record level data underlying the figures and tables in the report:<strong><br><br>Coverage and quality of open metadata for Dutch research output - report<br></strong></p> <p><a href="https://doi.org/10.5281/zenodo.10629457" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10629457</a><br><br>The current dataset contains 3 csv files:</p> <ul> <li><em>rpo_nl_list_long_20240201.csv</em> - list of identifiers (ROR ID, OpenAlex ID, OpenAIRE ID) of Dutch research performing organisations. <p>Identifiers were collected for the following groups of Dutch RPOs (see Appendix A):</p> <ul> <li> <p>Universities, organised in Universities of the Netherlands (UNL, n=14);</p> </li> <li> <p>University Medical Centres, organised in the Dutch Federation of University Medical Centres (NFU, n=9); </p> </li> <li> <p>National research institutes under the umbrella organisation of the Foundation for Dutch Scientific Research Institutes (NWO-i, n= 9);</p> </li> <li> <p>Research institutes of the Royal Netherlands Academy of Arts and Sciences (KNAW, n=10);</p> </li> <li> <p>Universities of Applied Sciences affiliated to the Netherlands Association of Universities of Applied Sciences (Vereniging Hogescholen) (VH, n=35 of 37)<br><br></p> </li> </ul> </li> <li><em>openalex_works_20231223_rpo_nl_2022 </em>- record-level data of OpenAlex records retrieved for all Dutch RPOs in scope of the pilot (UNL/NFU, NWO-i, KNAW, VH) for publication year 2022<br><br></li> <li><em>openaire_products_20240116_rpo_nl_2022 - </em>record-level data of OpenAlex records retrieved for all Dutch RPOs in scope of the pilot (UNL/NFU, NWO-i, KNAW, VH) for publication year 2022</li> </ul>
Data and Statistical analysis for: "Predator in the pool? A quantitative evaluation of non-indexed open access journals in aquaculture research"
<p>Data and Statistical analysis for: "Predator in the pool? A quantitative evaluation of non-indexed open access journals in aquaculture research" published in <em>Frontiers in Marine Science</em></p>
Resource Metadata Harvested from Government and Research Open Data Portals
<p>This dataset consists of resource metadata harvested from the APIs of hundreds of government and research data portals from all over the world. This dataset was harvested between the 13<sup>th</sup> and 15<sup>th</sup> of September 2018. The metadata harvested from these portals was translated to a single metadata format (see <em>metadata_format.odt</em>). An overview of all harvested domains is given in <em>portal_list.txt</em>.</p> <p>The harvested data is divided into five gzipped json-lines files, based on the ‘type’ of the resource that is derived from the data of the APIs:</p> <ul> <li><em>dataset_metadata.jsonl.gz</em>: Resources classified as a Dataset, or subsets of dataset (e.g. Dataset:Image and Dataset:Audio) [6 246 250 resources]</li> <li><em>document_metadata.jsonl.gz</em>: Resources classified as a Document, or subset of document (e.g. Document:Paper:Conference and Document:Book) [15 626 541 resources]</li> <li><em>software_metadata.jsonl.gz</em>: Resources classified as Sofware (including Software:Model) [42 036 resources]</li> <li><em>service_metadata.jsonl.gz</em>: Resources classified as a service (e.g. WMS, APIs) [1257 resources]</li> <li><em>other_metadata.jsonl.gz</em>: Resources of which the ‘type’ could not be determined from the data the API returned. This set still contains many datasets [1 502 979 resources]</li> </ul>
Toolkit on Open Access for Research Project Coordinators
<p>The materials in this toolkit were created by Romain Féret as a resource for training on how to help project coordinators to comply with their open access requirements. The slides of the training are available on Zenodo at 10.5281/zenodo.3381783. This training day took place on Wednesday the 5th of June 2019, at the University of Lille. It was organized with the support of Couperin as a part of its activities in the project OpenAIRE-Advanced.</p> <p>The tutorials are divided into two folders. The ‘Coordinator’ folder contains documents that can be sent directly to the researchers, while the ‘Support staff’ folder contains tutorials for support staff (librarians, project managers) who help the coordinators to manage their project. Each tutorial is in .pdf and .docx format for easy reuse and modification. Each document is available in French and in English.</p>
Evaluating Open Science Practices in Indoor Positioning and Indoor Navigation Research (Supplementary Material: Full Paper Listing and Analysis)
<p>Supplementary material of the paper:</p> <p>Title: "Evaluating Open Science Practices in Indoor Positioning and Indoor Navigation Research"<br>Subtitle: "A Survey of the IPIN's Reference Papers of 2022 and 2023 Editions"</p> <p>The paper is accepted to the "14th International Conference on Indoor Positioning and Indoor Navigation, IPIN 2024, Hong Kong, October 14-17, 2024, IEEE, 2024.</p> <p>An Author's accepted version of the manuscript is available here: <a href="../records/13684170" target="_blank" rel="noopener">https://zenodo.org/records/13684170</a> </p> <p>If you want to refer to this work, please cite this Zenodo entry as well as the published conference version.</p> <p> </p> <p>---------------------------------------</p> <p>This entry contains two files:</p> <ul> <li>"Paper Characterization Spreadsheet.xlsx": <strong>The spreadsheet of the full analysis of this work</strong>, as described in the paper. It characterizes various features of the analyzed papers and forms the raw data on which the analyses of our work were based.</li> <li>"Main features of the manuscripts analysed in Zenodo Record #12088175.pdf": A document summarizing the main features of the IPIN's Reference Papers of the 2022 and 2023 Editions, that contain some form of open resources (Open Data, Code, or Material).</li> </ul> <p> </p> <p> </p> <p> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.