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72 results for “scientific publications”
Figures in Scientific Open Access Publications - Underlying Data
<p>This publication contains data for a statistical analysis of an OA article corpus. The underlying dataset consists of over 1 million open access articles from different publishers (Copernicus: 9592; Springer:78418; Hindawi: 147848; Frontiers: 57621; PMC (aggregator): 747839)</p>
Biolinks, datasets and algorithms supporting semantic-based distribution and similarity for scientific publications
<p><strong>Background: </strong>Finding articles related to a publication of interest remains a challenge in the Life Sciences domain as the number of scientific publications grows day by day. Publication repositories such as PubMed and Elsevier provides a list of similar articles. There, similarity is commonly calculated based on title, abstract and some keywords assigned to articles. Here we present the datasets and algorithms used in Biolinks. Biolinks uses ontological concepts extracted from publication and makes it possible to calculate a distribution score according to semantic groups as well as a semantic similarity based on either all identified annotations or narrowed to one or more particular semantic groups. Biolinks supports both title and abstract only as well as full-text.</p> <p><strong>Materials: </strong>In a previous work [1], 4,240 articles from the TREC-05 collection [2] were selected. The title-and-abstract for those 4,240 articles were annotated with Unified Medical Language System (UMLS) concepts, such annotations are refer to as our TA-dataset and correspond to the JSON files under the pubmed folder in the JSON-LD.zip file. From those 4,240 articles, full-text was available for only 62. The title-and-abstract annotations for those 62 articles, TAFT-dataset, are located under the pubmed-pmc folder in the JSON-LD.zip file, which also contains the full-text annotations under the folder pmc, FT-dataset. The list corresponding to articles with title-and-abstract is found in the genomics.qrels.large.pubmed.onlyRelevants.titleAndAbstract.tsv file, while those with full-text are recorded in the genomics.qrels.large.pmc.onlyRelevants.fullContent.tsv file.</p> <p>Here we include the annotations on title and abstract as well as those for full-text for all our datasets (profiles.zip). We also provide the global similarity matrices (similarity.zip).</p> <p><strong>Methods:</strong> The TA-dataset was used to calculate the Information Gain (IG) according to the UMLS semantic groups, see IG_umls_groups.PMID.xlsx. A new grouping is proposed for Biolinks, see biolinks_groups.tsv. The IG was calculated for Biolinks groups as well, IG_biolinks_groups.PMID.xlsx, showing a improvement around 5%.</p> <p>In order to assess the similarity metric regarding the cohesion of TREC-05 groups, we used Silhouette Coefficient analyses. An additional dataset Stem-TAFT-dataset was used and compared to TAFT and FT datasets.</p> <p>Biolinks groups were used to calculate a semantic group distribution score for each article in all our datasets. A semantic similarity metric based on PubMed related articles [3] is also provided; the Biolinks groups can be used to narrow the similarity to one or more selected groups. All the corresponding algorithms are open-access and available on GitHub under the license Apache-2.0, a frozen version, biotea-io-parser-master.zip, is provided here. In order to facilitate the analysis of our datasets based on the annotations as well as the distribution and similarity scores, some web-based visualization components were created. All of them open-access and available in GitHub under the license Apache-2.0; frozen versions are provided here, see files biotea-vis-annotation-master.zip, biotea-vis-similarity-master.zip, biotea-vis-tooltip-master.zip and biotea-vis-topicDistribution-master.zip. These components are brought together by biotea-vis-biolinks-master.zip. A demo is provided at http://ljgarcia.github.io/biotea-biolinks/; this demo was built on top of GitHub pages, a frozen version of the gh-pages branch is provided here, see biotea-biolinks-gh-pages.zip.</p> <p><strong>Conclusions: </strong>Biolinks assigns a weight to each semantic group based on the annotations extracted from either title-and-abstract or full-text articles. It also measures similarity for a pair of documents using the semantic information. The distribution and similarity metrics can be narrowed to a subset of the semantic groups, enabling researchers to focus on what is more relevant to them.</p> <p> </p> <p>[1] Garcia Castro, L.J., R. Berlanga, and A. Garcia, <em>In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central Open Access.</em> Journal of Biomedical Informatics, 2015. <strong>57</strong>: p. 204-218</p> <p>[2] Text Retrieval Conference 2005 - Genomics Track. <em>TREC-05 Genomics Track ad hoc relevance judgement</em>. 2005 [cited 2016 23rd August]; Available from: http://trec.nist.gov/data/genomics/05/genomics.qrels.large.txt</p> <p>[3] Lin, J. and W.J. Wilbur, <em>PubMed related articles: a probabilistic topic-based model for content similarity.</em> BMC Bioinformatics, 2007. <strong>8</strong>(1): p. 423</p>
Improving access to and reuse of research results, publications and data for scientific purposes - Stakeholders' consultations results
<p>The data sets were created via data collection effort for the Horizon Europe-funded "study to evaluate the effects of the EU copyright framework on research and the effects of potential interventions and to identify and present relevant provisions for research in EU data and digital legislation, with a focus on rights and obligations". The study was contacted by DG RTD. </p> <p>This research project supports Action 2 objectives of the European Research Area (ERA) Policy Agenda 2022-2024, which aims to propose an EU legislative and regulatory framework for copyright and data that is fit for research. The report provides a comprehensive analysis of barriers to the access and reuse of publicly funded research, including scientific publications and data. It assesses existing EU copyright legislation and EU data and digital legislation. It also assesses regulatory frameworks and national initiatives and identifies potential areas for improvement.</p> <p>Using a methodological, evidence-based approach (including the survey results posted in this repository), the study presents possible legislative and non-legislative measures to improve the current EU copyright and data framework and align it with the needs of scientific research and open research data principles. </p> <p>The data sets include the raw data of the three surveys (survey 1 targeted at researchers, survey 2 targeted at research-performing organisations, and survey 3 targeted at publishers). All surveys have two major parts: one concerning copyright legislation and another concerning data and digital legislation. In addition, we provide interview notes, they are also organised into two parts: one concerning copyright legislation and another concerning data and digital legislation. </p> <p>The data collection effort was partially supported by our colleagues from the Institute for Information Law (IVIR) and KU Leuven CiTIP. </p>
Additional online material for publication: Frames and Narratives in scientific press releases on ocean climate change and ocean plastic.
<p>This is the additional material for the publication of paper: Frames and Narratives in scientific press releases on ocean climate change and ocean plastic. The paper is currently under submission. </p> <p>Included with the material is a codebook used to code narrative- and frame variables in scientific press releases and a cross-tabulate showing the frame variables that were coded per press release. </p> <p>For questions about the material, or information about how to reference to the material, please contact Aike Vonk (a.n.vonk@uu.nl).</p>
Datasets from Approximate equality of character strings and its application to record linkage in metadata of scientific publications thesis
<p>The datasets were produced in my thesis project. The thesis (in Czech language) explores the application of approximate string matching in scientific publication record linkage process. An introduction to record matching along with five commonly used metrics for string distance (Levenshtein, Jaro, Jaro-Winkler, Cosine distances and Jaccard coefficient) are provided. These metrics are applied on publication metadata from V3S current research information system of the Czech Technical University in Prague. Based on the findings, optimal thresholds in the F1, F2 and F3-measures are determined for each metric.</p> <p>Thesis citation:<br> DOBIÁŠOVSKÝ, Jan. <em>Approximate equality of character strings and its application to record linkage in metadata of scientific publications</em> [online]. Praha, 2020 [cit. 2020-05-04]. Masters thesis. Charles University. Faculty of Arts. Institute of Information Studies and Librarianship.</p> <p> </p>
Brazilian Scientific Publication Records and Author Affiliations from Lattes until Feb 2017 (Anonymized)
<p>This file contains anonymized data about researcher profiles and publication records available extracted from the Lattes Platform in in February 2017 using the LattesDataXplorer tool. Lattes is a vast repository of researchers' curriculum vitae, widely adopted in Brazil. This platform is maintained by the Brazilian National Council of Scientific and Technological Development (CNPq) and is an internationally renowned initiative.</p> <p>In the zipped file, there are two files:</p> <ul> <li>anon_authors.csv contains data about researchers. It has 3 columns <ul> <li>profile: researcher anonymized id</li> <li>instituition: researcher affiliation</li> <li>zipcode: institution zip code</li> </ul> </li> </ul> <ul> <li>anon_papers.csv contains data about researchers' publications. It has 4 columns: <ul> <li>profile: researcher anonymized id</li> <li>year: publication year</li> <li>venue: publication venue</li> <li>authors: number of authors</li> </ul> </li> </ul>
Disease and lesion maps - part of the Scientific opinion on the evaluation of public and animal health risks in case of a delayed post-mortem inspection in ungulates
<p>EFSA was requested to assess the impact on effectiveness of <em>post-mortem</em> inspection in terms of any change in the sensitivity of detection of animal diseases of domestic and wild ungulates listed according to Article 5 of Regulation (EC) No 2016/429 and septicaemia, pyaemia, toxaemia or viraemia, when carried out after up to 24 hours or up to 72 hours after slaughter in comparison to when it is carried out immediately after slaughter. In order to identify the main lesions associated with the target diseases, a so called “disease map” was built, with the information about the clinical forms of the diseases (acute, subacute, chronic, or latent forms) and clinical signs, as well as potential lesions that could be observed on the respective diseased animals.</p> <p>The following information is indicated for each disease/condition in the disease map:</p> <ol> <li>The susceptible animal species</li> <li>Whether there is any surveillance programme in place in the EU</li> <li>The signs associated with the disease that could be detected at <em>ante mortem </em>inspection;</li> <li>The lesions associated with the disease that could be detected at <em>post mortem</em> inspection</li> <li>The probability of detecting the disease during the PMI as normally carried out.</li> <li>Whether carcass swabbing and/or laboratory tests are normally carried out.</li> </ol> <p>From the disease map, the list of organs to be considered at <em>post mortem</em> inspection and the lesions, a “lesion map” was built by connecting animal species with organs, lesions and corresponding disease. This was done to facilitate the construction of a questionnaire where, for each organ and the five types of lesions, the respondents (meat inspectors) had to provide a numerical answer about how many carcasses out of 100 with the given lesion, will be still detected after 24- or 72-h of refrigerated storage.</p>
List of Twitter bots that mention scientific publications
<p>This collection of datasets comes from the paper titled <em>"The Botization of Science? Large-scale study of the presence and impact of Twitter bots in science dissemination"</em> and includes two files:</p> <ol> <li><strong>Twitter_bots_list.txt</strong> - Contains a list of 11,073 Twitter bots that mention scientific publications, as identified in the study.</li> <li> <p><strong>Twitter_botscores.tsv</strong> - Includes the botscores of 4,872,369 Twitter accounts analyzed in the study, providing a measure of the likelihood that an account is a bot.</p> </li> </ol>
PreprintMatch: a tool for preprint publication detection applied to analyze global inequities in scientific publishing
<p>Dataset underlying the paper "PreprintMatch: a tool for preprint publication detection applied to analyze global inequities in scientific publishing." preprint-paper-matches.csv lists all matches found by our algorithm between bioRxiv/medRxiv and PubMed, and preprint_affiliations.csv lists all extracted affiliations from bioRxiv/medRxiv. The Rxivist data dump (https://zenodo.org/record/4738007) was used for all preprint data, and the scrips to download PubMed data are available on our GitHub repository, https://github.com/PeterEckmann1/preprint-match.</p> <p>The full database dump, with all data used in the study, is available on Google Drive at https://drive.google.com/file/d/1ZoafhYUP-DO4Hd_4A_v7mbQLjN3JPzJv/view?usp=sharing. The PostgreSQL database can be restored using the pg_restore command.</p>
Data S1. Scientific Publication Data
<p>This dataset contains the number of scientific publications about mangroves in the thirteen most mangrove-rich countries and worldwide, by year, from 1975 to 2023. </p>
Data Matrix Theme-Specific Analysis of the Recommendation on Science and Scientific Researchers (RSSR): Public and Stakeholder Engagement
<p>This Table sets out findings from the mapping exercise conducted as part of the objectives of subtask 6.1 of the RRING project.</p> <p>Aim: Alignment of RRI to advance the UN SDGs.</p> <p>Objectives:</p> <ul> <li>Mapping the RSSR to the SDGs </li> </ul> <p>Mapping the RSSR to the SDGs is aimed at providing new perspectives, ideas and approaches that can help to improve the operationalization and implementation of each SDG, <em>by facilitating the integration of RRI (or RRI-like) practices in the SDGs, to make them more achievable.</em> The impact of the new perspectives, ideas and approaches in SDG operationalization and implementation will be aimed at the level of <em>national and international policy (making); future research and innovation projects (in industry and academia); as well as education and training of researchers, policy makers and other stakeholders.</em></p> <p>Two documents were used for this task:</p> <ul> <li>2017 Recommendation on Science and Scientific Researchers ([RSSR], UNESCO), and</li> <li>the United Nations 2030 Agenda for Sustainable Development with the 17 Sustainable Development Goals (SDGs).</li> </ul>
Data Availability Statements in the 2020 and 2021 scientific publications of Tampere University
<p>For this dataset, scientific peer-reviewed articles by Tampere University researchers from the years 2020 and 2021 were extracted from the TUNICRIS. A random sample of 40 percent was taken from the listed 4,922 publications according to faculties and years. There were 2,085 analyzed articles, i.e. more than 42 percent of the total number. </p> <p>To find Data Availability Statements, articles were opened one by one and searched for mentions of research data and its availability. For each article, it was written down whether DAS existed and where in the article it was located. From the contents of DAS, information about data availability, location, openness and possible restrictions on use was written down. </p> <p>Dataset also includes information about the journals and publications taken from TUNICRIS. </p> <p>The prevalence of DAS and data openness were examined in relation to different variables. Tampere University faculty information has been removed from the dataset. </p> <p>Related slides: https://doi.org/10.5281/zenodo.7655892</p> <p>Related article (in Finnish): Toikko, T., & Kylmälä, K. (2023). Tutkimusdatan saatavuustiedot tieteellisissä artikkeleissa: Raportti Data Availability Statementien käytöstä Tampereen yliopistossa. <em>Informaatiotutkimus</em>, 42(1-2), 31–50. https://doi.org/10.23978/inf.126098</p>
Services of AS CR Library in the area of scientific publications (not only) for AS CR Institutes
<p>Since 1994, the Library of the Academy of Sciences of the Czech Republic has been the coordinator of bibliographic database ASEP, which contains the records of publishing activities of 54 institutes of the Academy of Sciences of the Czech Republic (AS CR). Bibliographic records are collected in the Institatunional Repository of the ASCR, data is saved in the librarian system Advanced Rapid Library (ARL), the data is published as an on-line catalogue. The article describes how different groups of users – administrators, authors, representatives of institutes and AS CR can use this system. In details is decribed software ASEP Analytics which was created as a software extension that provides analytical reports derived by a combination of queries and calculations from the data stored in the ASEP database, which cannot be displayed directly in the catalogue.</p>
Public funding accountability: a linked open data-based methodology for analysing the scientific productivity and influence of funded projects. Dataset
<p>Tables containing the information about the projects funded by the Spanish AEI and publications acknowledging funding from Funder Registry. Both datasets where used in our publication: <em>Public funding accountability: a linked open data-based methodology for analysing the scientific productivity and influence of funded projects</em>.</p>
Research Funding in the Middle East and North Africa: Analyses of Acknowledgments in Scientific Publications (unified funders)
<p>This dataset is the result of the unification of funder names acknowledged in scientific publications indexed in the Web of Science with at least one author affiliated to an institution located in the Middle East and North Africa.</p> <p>This list contains 1,039 unified names of funders from the 22 MENA countries as of 16 March 2023 along with their type and country.</p>
Dataset for the publication Review of Scientific Instruments 92, 063205 (2021)
<p>Datasets for Fig. 3 and 5 of the publication "Long distance optical transport of ultracold atoms: A compact setup using a Moiré lens", Review of Scientific Instruments <strong>92</strong>, 063205 (2021)</p>
Scientific Webinar on Sustainable Public Food Procurement (SPFP) in the European Union
<p>On 23 April 2024, <a href="https://sapiensnetwork.eu/">SAPIENS Network</a> <a href="https://sapiensnetwork.eu/research/early-stage-researcher-projects/sustainability-to-collective-table/">Early Stage Researcher Chiara Falvo</a> held a scientific webinar focusing on Sustainable Public Food Procurement (SPFP) in the European Union. The event took place in hybrid form and was hosted within the Master’s Course in Food Systems Law at the Department of Law of the University of Turin, also in collaboration with the Department of Agricultural, Forestry and Food Sciences (DISAFA). After a brief introduction on public procurement law and practice, Chiara delved into the legal strategies and mechanisms for integrating social and environmental considerations into the procurement of food and catering services. She also highlighted some national and local experiences that are leading the way in the field. During the event, <a href="https://www.giurisprudenza.unito.it/do/docenti.pl/Alias?silvia.mirate#tab-profilo">Professor Silvia Mirate</a>, who also acted as a discussant, provided an overview on the new EU Deforestation Regulation (EUDR), followed by Chiara's exploration of its relevance for public procurement. Contributing to bridging the gap between the scientific domains of law and agricultural and forestry sciences, this webinar may be relevant for students and newcomers to public procurement, especially in the food sector, as well as for anyone interested in understanding deforestation issues and the latest legal mechanisms to combat them. </p>
Bibliography on criteria for assessing the quality of scientific publications
<p>The data deposited here consist of references to literature that was evaluated during the development of a qualitative survey and an online questionnaire on the qualitative perception of scientific publications.</p> <p>In preparation for these qualitative interviews and the online survey, a literature study on the qualitative perceptions of scientific literature was conducted in January and February 2018. The focus was on the question which internal characteristics, i.e. in the narrower sense content-related factors, influence the perception of a publication as qualitatively valuable or poor. External characteristics as citation counts should not be at the centre of the research - knowing that they control qualitative perception - since their effect on the perception of the quality of a publication is sufficiently discussed (see e.g. Dong, Loh, & Mondry, 2005).<br> The literature study was based on the results of a search in the databases Web of Science, Scopus, Library, Information Science & Technology Abstracts and the search engine Google Scholar.</p> <p>VisOA_full_results.bib includes references that were considered valuable in principle, VisOA.bib only those that have been considered in the development of the survey instruments.</p>
Data for publication 'Recreational vessels without Automatic Identification System (AIS) dominate anthropogenic noise contributions to a shallow water soundscape' (Scientific Reports 2019)
<p>Data on vessel tracks and underwater noise levels presented in the publication Hermannsen, L., Mikkelsen, L., Tougaard, J., Beedholm, K., Johnson, M. and P. T. Madsen, "Recreational vessels without Automatic Identification System (AIS) dominate anthropogenic noise contributions to a shallow water soundscape", Scientific Reports 9:15477 (<a href="https://doi.org/10.1038/s41598-019-51222-9">https://doi.org/10.1038/s41598-019-51222-9</a>).</p>
Repository of speech features from speakers with and without Parkinson's Disease. Neurovoz - Rasta PLP - V2 - Scientific Reports Publication: Phonetic relevance and phonemic grouping of speech in the automatic detection of Parkinson's Disease
<p>This repository contains the Rasta-PLP features of six different speech recordings (sentences) from Neurovoz corpus (47 parkinsonian and 32 control speakers whose mother tongue is Spanish Castillian.)<br> Number of PLP coefficients: [6, 8, 10, 12, 14, 16, 18, 20].<br> Delta coefficients: Yes<br> Delta Delta coefficients: Yes<br> Sampling rate: 16 kHz<br> Frame size: 15 ms<br> Frame overlapping: 50%</p> <p>This subset of the Neurovoz corpus was recorded between 2015 and 2017 by Universidad Politécncia de Madrid and Hospital General Universitario Gregorio Marañón.</p> <p>This version includes the same files as the previous version and information about UPDRS, H&Y, years since diagnosis and age of each participant.</p> <p>The sentences were:</p> <p>BARBAS: "Cuando las barbas de tu vecino veas pelar, pon las tuyas a remojar"</p> <p>CALLE: "De la calle vendrá quien de tu casa te echará"</p> <p>DIABLO: " Cuando el diablo no sabe qué hacer, con el rabo mata moscas "</p> <p>PETACA BLANCA: " La petaca blanca es mía"</p> <p>PIDIO: "No pidas a quien pidió ni sirvas a quien sirvió"</p> <p>SOMBRA: " El que a buen árbol se arrima, buena sombra le cobija "</p> <p> </p> <p>How to cite:<br> [1] Moro-Velazquez, L., Gomez-Garcia, J. A., Godino-Llorente, J. I., Grandas-Perez, F., Shattuck-Hufnagel, S. Yagüe-Jimenez, V., and Dehak, N. (2019). Phonetic relevance and phonemic grouping of speech in the automatic detection of Parkinson’s disease.Scientific reports 9, 19066.</p> <p><br> [2] Moro-Velazquez, L., Gomez-Garcia, J. A., Godino-Llorente, J. I., Villalba, J., Rusz, J., Shattuck-Hufnagel, S. and Dehak, N. (2019). A forced Gaussians based methodology for the differential evaluation of Parkinson's Disease by means of speech processing. Biomedical Signal Processing and Control, 48, 205-220.</p> <p>BibTeX:</p> <pre><code>@article{moro2019phonetic, title={Phonetic relevance and phonemic grouping of speech in the automatic detection of Parkinson's Disease}, author={Moro-Velazquez, Laureano and Gomez-Garcia, Jorge A. and Godino-Llorente, Juan I. and Grandas-Perez, Francisco and Shattuck-Hufnagel, Stefanie and Yague-Jimenez, Virginia and Dehak, Najim}, journal={Scientific Reports}, volume={9}, pages={19066}, year={2019}, publisher={Nature Research Publishing} } @article{moro2019forced, title={A forced Gaussians based methodology for the differential evaluation of Parkinson's Disease by means of speech processing}, author={Moro-Velazquez, Laureano and Gomez-Garcia, Jorge Andres and Godino-Llorente, Juan Ignacio and Dehak, Najim}, journal={Biomedical Signal Processing and Control}, pages={205--220}, volume={48}, year={2019}, publisher={Elsevier} } </code></pre> <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.