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8,537 results for “Openness”
SoK: Taxonomy of Attacks on Open-Source Software Supply Chains - Visualization Tool Screenshots & Selected Papers
<p>This artifact complements the paper "SoK: Taxonomy of Attacks on Open-Source Software Supply Chains", submitted at IEEE S&P 2023.</p> <p>The papers selected during the Systematic Literature Review (SLR) are presented in the CSV file.</p> <p>This screenshots display the main features of the visualization tool that allows to explore the taxonomy of attacks on OSS supply chains, as well as the related safeguards and the selected references.</p>
FAIR and Open multilingual clinical trials in Wikidata and Wikipedia
<p>"FAIR and Open multilingual clinical trials in Wikidata and Wikipedia" was a December 2021 presentation by Lane Rasberry and Cherrie Kwok. It was made at the conference "Understanding Wikipedia’s Dark Matter - Translation and Multilingual Practice in the World'’s Largest Online Encyclopaedia" hosted by the Centre for Translation and the Department of Translation, Interpreting and Intercultural Studies, both at Hong Kong Baptist University.</p> <ul> <li>conference page <a href="https://ctn.hkbu.edu.hk/wikiconf2021/">https://ctn.hkbu.edu.hk/wikiconf2021/</a></li> <li>watch video <a href="https://www.youtube.com/watch?v=5yRhCENeezQ">https://www.youtube.com/watch?v=5yRhCENeezQ</a></li> <li>slides archive <a href="https://commons.wikimedia.org/wiki/File:FAIR_and_Open_multilingual_clinical_trials_in_Wikidata_and_Wikipedia.pdf">https://commons.wikimedia.org/wiki/File:FAIR_and_Open_multilingual_clinical_trials_in_Wikidata_and_Wikipedia.pdf</a></li> </ul> <p> </p> <p> </p> <p> </p>
Analytics, Visualisation and Machine Learning of General Practitioner Prescribing using Open Health Data
<p>Open Prescription data used in Postgraduate project into Northern Ireland General Practice prescribing.</p>
Ocean surface wind estimation from waves based on small GPS buoy observations in a bay and the open ocean
<p>This is dataset of ocean surface wave and wind used in the paper "Ocean surface wind estimation from waves based on small GPS buoy observations in a bay and the open ocean" by Shimura et al. (2022, JGR-Oceans, <a href="https://doi.org/10.1029/2022JC018786">https://doi.org/10.1029/2022JC018786</a> ).</p> <p>"data_bayObservation.nc" contains the observed wind, estimated wind, and observed wave spectral data during the bay observations.</p> <p>"data_openOceanObservation.nc" contains the reanalysis wind, estimated wind, and observed wave spectral data during the open ocean observations.</p> <p> </p>
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
MapOSR - A Mapping Review Dataset of Empirical Studies on Open Science
<p>Research that investigates respective researchers’ engagement in Open Science varies widely in the topics addressed, methods employed, and disciplines investigated, which makes it difficult to integrate and compare its results. To investigate current outcomes of Open Science research, and to get a better understanding on topicswell-researched and on research gaps we aim at providing an openly accessible overview of empirical studies that focus on different aspects of Open Science in different scientific disciplines, academic groups and geographical regions. The present data set of studies about Open Science practices was retrieved following a PRISM approach to compile a literature review. We include studies from the Scopus and Web of Science databases with keywords relating to Open Science between the years 2000 and 2020, as well as a snowball search for relevant articles. Studies that did not investigate any aspect of Open Science, or weren’t peer reviewed were excluded, resulting in a total of 695 remaining studies. The data set was collaboratively annotated to ensure intercoder reliability of the coded data.</p>
Post-deposition annealing and interfacial ALD buffer layers of Sb2Se3/CdS stacks for reduced interface recombination and increased open-circuit voltages
<p>Data for the article:</p> <p>Post-deposition annealing and interfacial ALD buffer layers of Sb2Se3/CdS stacks for reduced interface recombination and increased open-circuit voltages</p>
Big in Japan, Zimbabwe or Brazil – global reach and national preferences for open access books
<p>When we consider the main differences in publication practices between the Humanities and Social Sciences (HSS) and Science Technology and Mathematics (STM) there are two aspects that almost always get mentioned: the prominence of books and the role of local languages. Not surprisingly, the work of HSS researchers written in in other languages than English is more often linked to more regional concerns or a more regional community. Simply put, an author using Dutch will have a different audience in mind than an author writing in English.</p> <p>The OAPEN Library contains thousands of open access monographs in dozens of languages and sees global usage. While books in English are in the majority – over 60% of the collection – this still leaves a large collection of publications in other languages. If a global audience can freely choose from this collection, will there be a preference for global subjects or will more regional concerns take preference? This explorative research will look at the most popular books from 100 countries and try to determine the level of regional interest.</p> <p>We will examine the preference of global readers in a systematic manner. Based on the ten most downloaded books from 100 countries during a 12 month period , the focus on regional topics will be measured in two ways: the amount of books written in non-English languages, and the amount of English language books that mention the country.</p>
Welcome to OR2015 : Open Repositories 2015 opening session
<pre>Opening session at Open Repositories 2015 (OR2015), the 10th International Conference on Open Repositories, Indianapolis, Indiana. Includes remarks by Jon Dunn (Organizing Committee Chair), Carol Minton Morris (Steering Committee Co-Chair), Carolyn Walters (Ruth Lilly Dean of University Libraries, Indiana University), William Nixon (Program Committee Co-Chair), Adam Field (Developer Challenge Co-Chair) and Claire Knowles (Developer Challenge Co-Chair). </pre>
Data from: Building communities of teaching practice and data-driven open education resources with NEON faculty mentoring networks
<p>With the growing availability and accessibility of big data in ecology, we face an urgent need to train the next generation of scientists in data science practices and tools. One of the biggest barriers for implementing a data-driven curriculum in undergraduate classrooms is the lack of training and support for educators to develop their own skills and time to incorporate these principles into existing courses or develop new ones. Alongside the research goals of the National Ecological Observatory Network (NEON), providing education and training are key components for building a community of scientists and users equipped to utilize large-scale ecological and environmental data. To address this need, the NEON Data Education Fellows program formed as a collaborative Faculty Mentoring Network (FMN) between scientists from NEON and university faculty interested in using NEON data and resources in their ecology classrooms. Like other FMNs, this group has two main goals: 1) to provide tools, resources, and support for faculty interested in developing data-driven curriculum, and (2) to make teaching materials that have been implemented and tested in the classroom available as open educational resources for other educators. We hosted this program using an open education and collaboration platform from the Quantitative Undergraduate Biology Education and Synthesis (QUBES) project. Here, we share lessons learned from facilitating five FMN cohorts and emphasize the successes, pitfalls, and opportunities for developing open education resources through community-driven collaborations.</p>
Open texbooks in France
<p>This session of the 2022 OE Week had be devoted to open access textbook projects developed in France. The project leaders will present their experience and the questions raised by their experiences. The session will be an opportunity to address issues related to economic models, editorial models and partnerships.<br> The session will take place on March 9, at 10:00 am. It will last 1 hour and 15 minutes, with time for questions and answers via chat at the end of the presentations.<br> Cette session sera consacrée à des projets de manuels en open access, développés en France. Les porteurs de projets présenteront leur expérience et les questions soulevées par leurs expériences. La session sera l'occasion d'aborder les questions liées aux modèles économiques, aux modèles éditoriaux et les partenariats.</p> <p>- Cécile Swiatek : "Open textbook within the framework of the Unesco policy"</p> <p>- Dorothée Pain : "An enhanced textbook in history"</p> <p>- Delphine Lereculeur : "Designing digital atlas"</p> <p>- Cédric Mercier : "Collaborations about energy transition"</p> <p>- Adrien Fauve : "EISCAS project : an European <a href="https://eiscas.eu/handbook/content/">Handbook</a> of Central Asian Studies"</p>
Metabolic syndrome for the prognosis of postoperative complications after open pancreatic surgery in Chinese adult: a propensity score matching study
<p><strong>Background: </strong>To investigate the relationship between metabolic syndrome (MS) and postoperative complications in Chinese adults after open pancreatic surgery.</p> <p><strong>Methods: </strong>Relevant data were retrieved from the Medicalsystem® database of Changhai hospital (MDCH). All patients who underwent pancreatectomy from January 2017 to May 2019 were included, and relevant data were collected and analyzed. A propensity score matching (PSM) and a multivariate generalized estimating equation were used to investigate the association between MS and composite compositions during hospitalization. Cox regression model was employed for survival analysis.</p> <p><strong>Results: </strong>1481 patients were finally eligible for this analysis. According to diagnostic criteria of Chinese MS, 235 patients were defined as MS, and the other 1246 patients were controls. After PSM, no association was found between MS and postoperative composite complications (OR: 0.958, 95%CI: 0.715-1.282, P=0.958). But MS was associated with postoperative acute kidney injury (OR: 1.730, 95%CI: 1.050-2.849, P=0.031). Postoperative AKI was associated with mortality in 30 days and 90 days after surgery (P<0.001).</p> <p><strong>Conclusions: </strong>MS is not an independent risk factor correlated with postoperative composite complications after open pancreatic surgery. But MS is an independent risk factor for postoperative AKI of pancreatic surgery in Chinese population, and AKI is associated with survival after surgery.</p>
Spectrum of Open Methods
<p>In order for Open Methods to mitigate resource barriers to linguistics research, the Open Methods themselves must not act as or require <em>substantial</em> resource barriers to access and use. We emphasize "substantial" here because there is no such thing as an absence of resource barriers; just because an Open Method is freely <em>available</em> online doesn't make it <em>accessible</em> to everyone. To evaluate this aspect of Open Methods, we build on similar widely-used tools in the Open Access space to create a "Spectrum of Open Methods".</p> <p>This tool is not meant to gatekeep open methods; a method that's imperfect but published is always more open than a method that never gets published because it's not perfect yet. Rather, the Spectrum of Open Methods is intended to inspire creators to make adjustments to their resources to make them as open as possible. To illustrate, a Case Study is included where Dan Villarreal has deployed the Spectrum of Open Methods to one of his projects and identified avenues for future development and improvement.</p> <p>We developed this tool while working on a chapter titled "Open Methods: Decolonizing (or not) research methods in linguistics" for the forthcoming volume <em>Decolonizing Linguistics </em>edited by Anne Charity Hudley, Christine Mallinson, and Mary Bucholtz and published by Oxford University Press. We welcome iterations of this Spectrum of Open Methods with edits, adaptations to other fields, or discipline-specific adjustments.</p>
Open habitats in a tropical biodiversity hotspot support pollinator diversity in both protected and unprotected areas
<p class="MsoNormal">Protected areas (PAs) are vital in the global effort to preserve biodiversity, particularly for disturbance-intolerant pollinator species in the tropics. As there is little information on the potential of PAs for pollinator conservation in sensitive tropical ecosystems, we assessed here insect pollinator diversity in protected vs. unprotected areas in two vegetation zones in Nigeria, within the West African Guinea Biodiversity Hotspot. We selected two land-use types based on predominant canopy cover type (open and tree-shaded habitats) and these were sampled in both protected and unprotected areas of tropical rain forest and savanna vegetation zones. Pollinator composition varied significantly between protected vs. unprotected areas in each vegetation zone, signifying both areas support unique assemblages of insect pollinators. However, pollinator diversity varied according to land-use type (open vs. shaded habitats) rather than protected area per se, such that pollinators were more abundant and species-rich in open habitat than shaded habitat. These findings emphasize that beyond the protection of ecosystems, fine scale habitat management promoting the availability of adequate floral resources in natural areas is critical for ensuring conservation of these pollinators in tropical ecosystems. </p>
Scoping survey on the state of play of Open Science at SEA-EU universities
<p>Survey data that sought to collect information about the state of play on Open Research Data Management practices amongst the SEA-EU Alliance.</p>
Documenting And Assessing Open Innovation: Co-creation Of An Open Data Model For Surgical Training (Additional materials, tables 2 & 3)
<p>Challenge competitions have recently resurged for promoting open innovation in areas where markets fail to provide incentives, such as the Sustainable Development Goals (SDGs). Challenges call for the general public to contribute novel solutions to a well-defined problem, in exchange for prizes, credentials and the promise of further development of selected solutions. The aim of this paper is to report on the development of an open and collaborative data model to document and evaluate innovations in the context of a challenge competition, while also being compatible with the work of other open source communities to validate and improve them. By reusing open documentation standards and embedding them into a semantic collaborative platform, the model aimed to be flexible enough to respond to the evaluation needs of the project organisers and self-assessment for participants. We expect our experience provides insights on the potential of semantic, collaborative platforms and standards for increasing the impact of innovations towards the SDGs.</p> <p>The developer team defined the goal and scope of the ontology in collaboration with the GSTC organisers. This was done by agreeing on scenarios where the ontology will be used and establishing competency questions that the ontology has to be able to respond to. Table 2 describes the four motivating scenarios, including actors involved, requirements, sequence of actions and main problems identified. Table 3 details the competency questions for each scenario.</p>
Data for blog post on dfm.io: "An experiment in open science: exoplanet population inference"
<p>The data set used be the blog post "An experiment in open science: exoplanet population inference" published at https://dfm.io/posts/exopop/</p>
An open-access database of infectious disease transmission trees to explore superspreader epidemiology
Historically, emerging and reemerging infectious diseases have caused large, deadly, and expensive multinational outbreaks. Often outbreak investigations aim to identify who infected whom by reconstructing the outbreak transmission tree, which visualizes transmission between individuals as a network with nodes representing individuals and branches representing transmission from person to person. We compiled a database, called OutbreakTrees, of 382 published, standardized transmission trees consisting of 16 directly transmitted diseases ranging in size from 2 to 286 cases. For each tree and disease, we calculated several key statistics, such as tree size, average number of secondary infections, the dispersion parameter, and the proportion of cases considered superspreaders, and examined how these statistics varied over the course of each outbreak and under different assumptions about the completeness of outbreak investigations. We demonstrated the potential utility of the database through 2 short analyses addressing questions about superspreader epidemiology for a variety of diseases, including Coronavirus Disease 2019 (COVID-19). First, we found that our transmission trees were consistent with theory predicting that intermediate dispersion parameters give rise to the highest proportion of cases causing superspreading events. Additionally, we investigated patterns in how superspreaders are infected. Across trees with more than 1 superspreader, we found preliminary support for the theory that superspreaders generate other superspreaders. In sum, our findings put the role of superspreading in COVID-19 transmission in perspective with that of other diseases and suggest an approach to further research regarding the generation of superspreaders. These data have been made openly available to encourage reuse and further scientific inquiry.
Complementary dataset of Overton metadata on citing policy-related documents for the study "From intent to impact: Investigating the effects of open sharing commitments"
<p>This document provides the underlying dataset for the bibliometric component for the 2022 study "From intent to impact: Investigating the effects of open sharing commitments" by Research Consulting and Science-Metrix.</p> <p>Before reproducing the study findings or re-using the underlying datasets for other purposes, please cautiously review their limitations in the study's technical annex and main report, available at: https://zenodo.org/communities/data-sharing-in-public-health-emergencies/ </p> <p>Special thanks from the Science-Metrix / Elsevier teams to Euan Adie and Overton for this exceptional public release of Overton metadata, and for conducting extraordinary data collection to retrieve citations towards arXiv preprints.</p> <p> </p> <p>Scope: note that this file combines cited journal publications and preprints from the Covid19, HVRD, Zika and HVVD thematic sets.</p> <p>Data treatment: this data is intend foremost to provide manual validation or qualitative triangulation of our findings. No special efforts have been made to process and clean the data for its eventual re-use in secondary analysis or text mining approaches.</p> <p>Definitions used in this table:</p> <table> <tbody> <tr> <td>Column name </td> <td>Definition</td> </tr> <tr> <td>document_type</td> <td>preprint or journal publication</td> </tr> <tr> <td>doi</td> <td>digital object identifier</td> </tr> <tr> <td>arxiv_id</td> <td>arXiv preprint server's unique identifier for its preprints</td> </tr> <tr> <td>ssrn_id</td> <td>SSRN preprint server's unique identifier for its preprints. Note that some of these IDs are contained within the DOIs also assigned to some (but not all) SSRN preprints , in the form of "10.2139/ssrn." + 'ssrn_id'</td> </tr> <tr> <td>coalesce_id</td> <td>coalesce function applied to the DOI, arxiv_id and ssrn_id. Redundant for journal publications.</td> </tr> <tr> <td>policy_source_title</td> <td>name of the policy-related organization</td> </tr> <tr> <td>published_on</td> <td>publication date of the citing policy-related document</td> </tr> <tr> <td>title</td> <td>title of the citing policy-related document</td> </tr> <tr> <td>pdf_url</td> <td>URL for the online version of the policy-related document</td> </tr> <tr> <td>snippet</td> <td>Where available, excerpt of the text immediatly before and after the citation to a journal publication or preprint found in the citing policy-related document</td> </tr> </tbody> </table> <p> </p>
Webinar "Citizen Involvement in Open Science: Roles, Levels and Opportunities", May 26, 2022
<p>LibOCS Webinar “Citizen Involvement in Open Science: Roles, Levels and Opportunities”, May 26, 2022.</p> <p>PR2 milestone - information campaign. </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.