Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
8,537
datasets available to search
ShareScore release 0.9.0
Dataset results
8,537 results for “Openness”
Digital Community Heritage and Open Access Dataset
<p>Dataset containing 27 digital community heritage initiatives, defined as online initiatives where community members or users contribute to a community heritage-related common cause, which promotes the interests of the community(ies) and/or the greater public.</p> <p>Access the report: Ziku, M., & Fabos, B. (2022). Digital Community Heritage and Open Access. CC Open Culture Working Group Digital Community Heritage. https://doi.org/10.21428/9eb74dbf.0c46e6be</p>
Open-source Software Governance Documentation Dataset on GitHub
<p>This dataset contains 710 GitHub-hosted OSS projects, which contain a governance file in the root directory of the project. It also contains commits, issues, and comments on each project.</p>
The LOTUS Initiative for Open Natural Products Research: TMAP
<p>TMAP of the compounds present on Wikidata curated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
Challenges and directions for open ecosystems biodiversity restoration: An overview of the techniques applied for Cerrado
<p>1. Ecological restoration of tropical open ecosystems remains challenging for both science and practice. Over the last decade, innovative techniques have been developed, but whether they have been successful or not remains to be demonstrated. Assessing the outcomes of these initiatives is crucial to drive the following steps to improve tropical grasslands and savanna restoration.</p> <p>2. Analyzing 82 data sets from the literature and primary data collection, we assessed the effectiveness of passive and active restoration techniques applied in Cerrado open ecosystems. We used plant diversity variables (species and growth forms) as indicators, considering ruderals and exotics as non-target species. Specifically, we aimed to answer: (i) How does the diversity of target species change through time in areas subject to passive restoration? (ii) Are active and passive restoration techniques effective in restoring the proportion of target species found in old-growth reference ecosystems? (iii) Have the current techniques been successful in recovering the proportions of growth forms of reference ecosystems?</p> <p>3. We found that target species proportions do not increase with time, suggesting limitations of typical species to colonize degraded sites. Hence, passive restoration will promote the conservation of a limited and constant number of target species. This number will depend on the magnitude of degradation and previous land use.</p> <p>4. The restoration techniques currently applied to restore the biodiversity of Cerrado open ecosystems are not reaching the reference standards, with distinct techniques driving plant communities to different sets of growth forms. Active restoration based on propagules obtained from pristine donor sites (topsoil translocation, plant material transplant, and seeding) performed better than passive restoration for most of the growth forms analyzed.</p> <p>5. Synthesis and Applications: Different growth forms have different roles in determining the structure and functioning of Cerrado vegetation. A mix of techniques can better approximate plant diversity and the proportionality of target species of pristine ecosystems. Singular restoration approaches are insufficient for restoring Cerrado open ecosystem biodiversity. Mixed efforts encompassing various techniques are required instead. Furthermore, it is likely restoration success can be improved with greater investment in improving our understanding of and developing existing restoration techniques.</p>
Annotated necrosis and mitotic figures on 230 rat liver slides of the Open TG-GATEs dataset
<pre># Annotated necrosis and mitotic figures on 230 rat liver slides of the Open TG-GATEs dataset This dataset contains polygonal annotations of 230 whole slide images of the Open TG-GATEs dataset. The annotations were created by Bayer pathologists in a project collaboration between Bayer Pharmaceuticals and Aignostics GmbH. ## Dataset Files This dataset contains only text files which are referring to whole slide images of the Open TG-GATEs dataset. The images are not distributed with this dataset. Image URLs and their respective `md5` checksums are stored in `slides.json`. The annotations are available in the raw json format used in the collaboration as well as in converted [`geojson`](https://geojson.org/) format for easy import into other tools. | file | description | |:-----------------------------------|:-------------------------------------| | slides.json | URLs/md5-checksums of each slide | | annotations/raw/\*.svs.json | original format tissue annotations | | annotations/geojson/\*.svs.geojson | tissue annotations in geojson format | ## Annotated Lesions / Classes The dataset was annotated by 6 expert pathologists with the goal of labelling "Necrosis" and "Mitotic Figures" on rat liver whole slide images. Additional areas in the slides were labelled to improve model training. An overview of the annotated classes is given in the table below: | label | count | area (px^2) | |:---------------------------------------------------|------:|-------------:| | Necrosis (area) | 1576 | 386769004.0 | | Necrosis (single cell) | 1497 | 1624837.5 | | Mitosis | 5205 | 9322482.0 | | Single cell necrosis/apoptosis | 1531 | 1446001.0 | | Central vein | 1125 | 27947588.0 | | Connective tissue | 63 | 8478992.5 | | Dark hepatocytes | 763 | 2516812.5 | | Extramedullary hematopoiesis | 73 | 189508.0 | | Hemorrhage | 142 | 2231979.0 | | Inflammatory infiltrate | 1382 | 9859337.5 | | Large vessels | 224 | 597148962.0 | | Neoplasia | 176 | 478842.5 | | Oval cell/bile duct proliferation | 47 | 1621104.5 | | Parenchyma | 3249 | 673395978.0 | | Portal tract | 1067 | 40819943.0 | | Other lesions | 5 | 9251.0 | | Staining, contamination, and out-of-focus artifact | 46 | 4484697.0 | The pathologists labeled the following number of lesions: | pathologist | annotations | |:--------------|------------:| | pathologist-0 | 15660 | | pathologist-1 | 1749 | | pathologist-2 | 660 | | pathologist-3 | 79 | | pathologist-4 | 22 | | pathologist-5 | 1 | ## Reference The 230 slides of the Open TG-GATEs Pathological Image Database which the annotations refer to are part of the `Toxicogenomics Project and Toxicogenomics Informatics Project under CC Attribution-Share Alike 2.1 Japan` (`CC-BY-SA-2.1-JP`) and are available for download via [10.18908/lsdba.nbdc00954-02-000](http://doi.org/10.18908/lsdba.nbdc00954-02-000). ## License All `*.json` and `*.geojson` files in this distribution are licensed under the same `CC Attribution-Share Alike 2.1 Japan` (`CC-BY-SA-2.1-JP`) license as the Open TG-GATEs Pathological Image Database. The license text is included in the file `LICENSE` in the distribution archive. ## Acknowledgements We thank Dr. Maximilian Alber[^5], Olivér Atanaszov[^5] and Dr. Sharon Ruane[^5] for providing support, the annotation platform, the model training infrastructure and for the great collaboration. We also thank Dr. Yoshinobu Igarashi[^6] for providing insight and advice regarding the dataset and its licensing. [^5]: Aignostics GmbH [^6]: National Institutes of Biomedical Innovation, Health and Nutrition - Toxicogenomics Informatics Project </pre>
Private vehicles greenhouse gas emissions at street level for Berlin based on open data
<p>We estimated the annual average daily GHG emissions from individual motor traffic for the OSM road network in Berlin by combining the estimated Annual Average Daily Traffic Volume (AADTV) with respective emission factors. The AADTV was calculated by simulating car trips with the open routing engine Openrouteservice, weighted by activity functions based on statistics of the German Mobility Panel.</p>
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field
<p>OpenFF Industry Public Dataset optimized at the (1) B3LYP-D3BJ / DZVP; (2) OpenFF-2.0.0; (3) Gaff-2.11-AM1BCC; (3) OPLS4 + default parameters; (4) OPLS4 + custom parameters.</p> <p>For (1) the corresponding tar.gz archive contains (a) sdf files of the final, optimized geometries and (b) json files with molecular properties of the final step of the optimization.</p> <p>For (2-4) the corresponding tar.gz archive contains sdf files of the final, optimized geometries.</p> <p>Note: The optimization carried out with both OPLS4 including default and custom parameters (4) was performed using the ffld_server to include virtual sites.</p>
WorldCereal open global harmonized reference data repository (CC-BY-NC licensed data sets)
<p>Within the <strong>ESA funded</strong> WorldCereal project we have built an open harmonized reference data repository at global extent for model training or product validation in support of land cover and crop type mapping. Data from 2017 onwards were collected from many different sources and then harmonized, annotated and evaluated. These steps are explained in the harmonization protocol (10.5281/zenodo.7584463). This protocol also clarifies the naming convention of the shape files and the WorldCereal attributes (LC, CT, IRR, valtime and sampleID) that were added to the original data sets.</p> <p>This publication includes those harmonized data sets of which the original data set was published under the CC-BY-NC license or a license similar to CC-BY-NC. See document "_In-situ-data-World-Cereal - license - CC-BY-NC.pdf" for an overview of the original data sets. Currently this publication only includes a few small data sets for Tanzania originating from a disease monitoring program of the International Maize and Wheat Improvement Center (CIMMYT). CIMMYT made more data available for countries like Kenya, Ethiopia, Rwanda and, Malawi. However due project contraints these data sets were not yet harmonized.</p>
Choosing Open Access Publishing: The Key Issues
<p>In this interactive webinar aimed at PhD students, post-docs and other early career researchers, <strong>Professor Patrick Dunleavy</strong> and <strong>Dr Frances Pinter </strong>introduced participants to Open Access Book Publishing, answered questions concerning the current publishing landscape, and gave insight into career-related issues for junior researchers to consider when choosing to publish open access. Although aimed specifically at junior researchers, this online webinar was open to all who wished to participate from across the CIVICA partner institutions.</p>
Preparing your thesis for an Open Access Repository
<p>The presenters gave participants a helpful overview prior to submitting their PhD thesis to LSE Theses Online and making it open access. Their presentation answered such questions as:</p> <ul> <li>What do you need to know about using copyright material in your PhD thesis?</li> <li>How does making your PhD thesis available on LSETO benefit you?</li> <li>What are the implications for your publishing plans?</li> </ul>
Proof of Concept database with inputs and outputs of the Master thesis: Analyzing Software Delivery Performance behavior in popular Open Source Software Projects on a Release timeline basis through delivery metrics
<p>The software has become one of the main assets to deliver services today. Thus, software delivery has been dealing with a competitive and dynamic environment where the demand for faster and more assertive deliverables, called here Releases, only increases. Agile development methods emerged helping to accelerate software delivery, embracing industry and open source community. Since then, the software delivery frequency has expanded and improved bringing more adopters of rapid release cycles to reduce their time-to-market. However, using only rapid releases can not be enough as measuring software delivery can answer essential questions, like how software delivery is happening and how it should be. Some approaches for measuring software delivery appeared such as Software Delivery Performance (SDP) where software delivery is measured as a consequence of capabilities evolution. Popularity in Open Source Software Projects (OSSP) means that a project is mature enough in the community to fit the software demand and, therefore, is likely to be ready to be measured through a software delivery approach like SDP. In light of it, this work offers means to analyze SDP behavior in popular Open Source Software Projects on a Release timeline basis through delivery metrics. The results demonstrated that popularity is efficient filtering, as it improves the OSSP delivery, supporting the work's reliability and accuracy. The source code and methodology are published as a replication package to encourage reproducibility and future research.</p>
Open Language Access (OLA): Democratising Linguistic Resources
<p>The audio file is a podcast introducing the Open Language Access (OLA) project.</p> <p>OLA is a collaborative digital archive that brings together researchers from all over the world. Launched in 2019 in the context of linguistic research, OLA is not just an archive but, above all, a platform that aims at providing tools for the creation, collaborative editing, exploration and publication of textual archives. In today's society, language stands as a central tool for change, and at the same time as a register and trace of the change itself. Hence the need to create a digital and accessible linguistic archive (open source and open access) with the aim of changing the paradigms of society's observation by providing an accessible tool to anyone who wants to look at change through language.</p>
MALDI-MS dataset for use with open-source untargeted metabolomic workflow for complex biological samples
<p class="MsoNormal">Untargeted metabolomics is a powerful tool for measuring and understanding complex biological chemistries. However, employment, bioinformatics and downstream analysis of mass spectrometry (MS) data can be daunting for inexperienced users. Numerous open-source and free to-use data processing and analysis tools exist for various untargeted MS approaches, but choosing the 'correct' pipeline isn't straight-forward. This data set can be used in conjunction with a user-friendly online guide which presents a workflow for connecting these tools to process, analyse and annotate various untargeted MS datasets. The workflow is intended to guide exploratory analysis in order to inform decision-making regarding costly and time-consuming downstream targeted MS approaches. The workflow provides practical advice concerning experimental design, organisation of data and downstream analysis, and offers details on sharing and storing valuable MS data for posterity. The workflow is editable and modular, allowing flexibility for updated/ changing methodologies and increased clarity and detail as user participation becomes more common allowing contributions and improvements to the workflow via the online repository. </p>
Factors influencing open government data post-adoption in the public sector: The perspective of data providers
Providing access to non-confidential government data to the public is one of the initiatives adopted by many governments today to embrace government transparency practices. The initiative of publishing non-confidential government data for the public to use and re-use without restrictions is known as Open Government Data (OGD). Nevertheless, after several years after its inception, the direction of OGD implementation remains uncertain. The extant literature on OGD adoption concentrates primarily on identifying factors influencing adoption decisions. Yet, studies on the underlying factors influencing OGD after the adoption phase are scarce. Based on these issues, this study investigated the post-adoption of OGD in the public sector, particularly the data provider agencies. The OGD post-adoption framework is crafted by anchoring the Technology–Organization–Environment (TOE) framework and the innovation adoption process theory. The data was collected from 266 government agencies in the Malaysian public sector. This study employed the partial least square-structural equation modeling as the statistical technique for factor analysis. The results indicate that two factors from the organizational context (top management support, organizational culture) and two from the technological context (complexity, relative advantage) have a significant contribution to the post-adoption of OGD in the public sector. The contribution of this study is threefold: theoretical, conceptual, and practical. This study contributed theoretically by introducing the post-adoption framework of OGD that comprises the acceptance, routinization, and infusion stages. As the majority of OGD adoption studies conclude their analysis at the adoption (decisions) phase, this study gives novel insight to extend the analysis into unexplored territory, specifically the post-adoption phase. Conceptually, this study presents two new factors in the environmental context to be explored in the OGD adoption study, namely, the data demand and incentives. The fact that data providers are not influenced by data requests from the agency's external environment and incentive offerings is something that needs further investigation. In practicality, the findings of this study are anticipated to assist policymakers in strategizing for long-term OGD implementation from the data provider's perspective. This effort is crucial to ensure that the OGD initiatives will be incorporated into the public sector's service thrust and become one of the digital government services provided to the citizen.
Agape Open Science MOOC
<p>Under Agape we aim to disseminate open science between PhD students and early career researchers across Ireland and later internationally. We want to create an open science practising community where we can learn, exchange our opinions and experiences, and together change the future. In the way that science is undertaken, made freely available, and communicated in a FAIR and transparent way.</p> <p> </p>
Nipah virus: Analysis of the scientific production in Open Access on the Web of Science, 2000 - 2020
<p>Data used in the analysis of the scientific production of Nipah in open access in the period 2000 to 2020</p>
Open data for publication: Advanced catalyst for CO2 photo-reduction: From controllable product selectivity by architecture engineering to improving charge transfer using stabilized Au clusters
<p>Original data for publication: Advanced catalyst for CO2 photo-reduction: From controllable product selectivity by architecture engineering to improving charge transfer using stabilized Au clusters, published in Small, 2023.</p> <p>The dataset is organized according to the Figures in the manuscript.</p>
The way forward with inclusive Open Science
<p>Presentation slides used during AAAS 2023 panel discussion session title: <a href="https://aaas.confex.com/aaas/2023/meetingapp.cgi/Session/30038">Foster Inclusion in Scientific Communities through Shared Data </a></p> <p>Synopsis:</p> <p>Over the past few years the scientific community has learned s=valuable lessons: It is stronger together; it must uplift one another in order to achieve scientific progress; and the best solutions are found when working together. But these lessons will be unable to spread very far unless all address the hesitancy in transitioning towards sharing data and results and the lack of applied experience with tools which make open collaboration easier. Transform to Open Science (TOPS) is a new National Aeronautics and Space Administration (NASA) Science Mission Directorate mission designed to spark a cultural shift to collaborative, inclusive science. Open science increases access to knowledge and expands opportunities for new voices to participate. Sharing the data, code, and knowledge associated with the scientific process lowers barriers to entry for historically-underrepresented communities, enables findings to be more easily reproduced, and generates new knowledge at scale. Success depends on everyone working to change the frameworks from which all operate. This session panel shows how open science is transformative and empowering for those who have traditionally been marginalized in science, technology, engineering, and math (STEM). The session highlights students and researchers of diverse backgrounds to share their open science experiences, including their foray into open science, barriers to practicing open science, and successes obtained through an open science framework.</p> <p>-----</p> <p>Abstract: <a href="https://aaas.confex.com/aaas/2023/meetingapp.cgi/Paper/31052">The way forward with inclusive Open Science</a></p> <p>Open science is an ethos behind communities that are intrinsically motivated to contribute to the greater good of humanity. Working openly is a way of building bridges with the larger scientific community creating more inclusive pathways for those looking to expand beyond their bounds. This in itself serves as a lifeline to many in marginalized communities, offering abundant opportunities for growth and development. Open science is not just for those who can, but also for those who can’t. </p>
Checklist v. 1.0 - Survey volcanic crises exercises: from open-question questionnaires to a prototype checklist
<p>Volcanic crisis exercises are usually run to test response capabilities, communication protocols, and decision-making procedures by those agencies, such as volcano observatories and/or Civil Protection authorities, with responsibilities to cope with scenarios of volcanic unrest with inherent uncertainty. During the last decades, the use of questionnaires has been increased to evaluate people’s knowledge on volcanic hazards and their perception of risk, which could affect their preparedness to respond to emergency measures plans. In this paper, we show the study carried out within the EUROVOLC European project focused on extracting information on the experience gained during volcanic-crisis exercises by the project’s participants and beyond. In particular, we first distributed an open-question questionnaire survey within the project community. Based on the results obtained, we developed a more user-friendly online multi-choice questionnaire that was submitted to different volcanological communities within and outside the project. From the answers to the on-line questionnaire, we extracted a prototype checklist for guiding those who need to design such exercises in the future. Here, we give details on the lessons learnt from this study, in particular about the need to increase training activities, to improve external (between players and general public/media) communication tools, equipment and protocols and to better define decision-makers' needs. Our preliminary results confirm that this type of survey is a very useful tool for gathering information on participants' experience and knowledge, and to understand which data and information may be useful when designing exercises for scientists, emergency managers and others involved in a volcanic crisis. </p>
Movie of the molecular dynamics simulation of the opening and closing of the Cullin-RING protein complex
<p>Heterobifunctional degraders, which consist of two separate protein binding moieties (the warhead and the E3-ligand) joined by a linker, are a class of molecules that "induce proximity" between a target protein of interest (POI) and a E3 ubiquitin ligase. This induced proximity can lead to ubiquitination of the POI and its subsequent proteosomal degradation through a complex machinery of proteins. TPD present a novel approach to drug protein targets, since a single degrader molecule can induce catalytic degradation of the POI and potentially offer an avenue to eliminate targets traditionally labeled as undruggable by classical therapeutic strategies. Here we probe the conformational landscape of the full CRL macromolecular assembly and present a MP4 trajectory movie showing the molecular dynamics simulation of the large-scale conformational change during the opening and closing of the Cullin-RING protein complex.</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.