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43 results for “persistent identifier”
Dataset to "Persistent Identifiers for File Formats: enabling preservation and re-use of research data"
<p>This fileset includes a "preprint" and the main dataset <em>fileformatRecognizer</em> (as .xlsx and .csv) to the paper "Persistent identifiers for file formats: enabling preservation and re-use of research data" submitted to iPRES 2019, but subsequently rejected after peer review. For the sake of transparency, permission to make available here the anonymous reviews motivating the rejection (<em>ReviewsPIDs4fileFormats.odt</em>) was asked, but was left without response. Some images (screendumps) and text result files from file identification tools tested are included. Further, a simple xquery command file (BaseX) for <em>fetch:content-type</em>()<em>, </em>used for getting MIME-types for files, is also provided.</p>
Multi-omics identify LRRC15 as a COVID-19 severity predictor and persistent pro-thrombotic signals in convalescence
<p>RNA sequencing, SomaLogic proteomics and flow cytometry data were generated for two cohorts of end-stage kidney disease patients with COVID-19. The Wave 1 cohort consists of samples collected from patients during the first wave of COVID-19 in early 2020, while samples were collected for the Wave 2 cohort in the following year.</p> <p>This data deposition includes the RNA-seq counts, SomaScan proteomics, flow cytometry and clinical metadata associated with the study. For further information about the study and data, see the associated GitHub repository (https://github.com/jackgisby/covid-longitudinal-multi-omics) or our pre-print (https://doi.org/10.1101/2022.04.29.22274267). The repository also contains code to replicate our analysis of the data.</p> <p>The raw RNA-seq reads were processed using the nf-core RNA-seq v3.2 pipeline before htseq-count was used to generate a raw counts matrix, which is included in this deposition (<code>htseq_counts.csv</code>). Three files make up the proteomics data: <code>sample_technical_meta.csv</code>, <code>feature_meta.csv</code> and <code>soma_abundance.csv</code>. The first two files contain metadata columns for the samples and protein features, respectively. The final file includes the unprocessed protein abundance data. The files <code>general_panel.csv</code> and <code>t_cell_panel.csv</code> contain the flow cytometry data, split into the general and T-cell panels, respectively. Finally, clinical metadata is available for the two cohorts described in this study (<code>w1_metadata.csv</code>, <code>w2_metadata.csv</code>).</p> <p>The features in the clinical metadata include:</p> <table> <thead> <tr> <th>Column Name</th> <th>Data Type</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>sample_id</td> <td>Character</td> <td>Unique identifier for samples</td> </tr> <tr> <td>individual_id</td> <td>Character</td> <td>Unique identifier for individuals</td> </tr> <tr> <td>ethnicity</td> <td>Character</td> <td>The individual's ethnicity (asian, white, black or other)</td> </tr> <tr> <td>sex</td> <td>Character</td> <td>The individual's sex (M or F)</td> </tr> <tr> <td>calc_age</td> <td>Integer</td> <td>Age in years</td> </tr> <tr> <td>ihd</td> <td>Character</td> <td>Information on coronary heart disease</td> </tr> <tr> <td>previous_vte</td> <td>Character</td> <td>Whether individuals have had venous thromboembolism</td> </tr> <tr> <td>copd</td> <td>Character</td> <td>Whether individuals have chronic obstructive pulmonary disease</td> </tr> <tr> <td>diabetes</td> <td>Character</td> <td>Whether individuals have diabetes, and, if so, the type of diabetes</td> </tr> <tr> <td>smoking</td> <td>Character</td> <td>Smoking status</td> </tr> <tr> <td>cause_eskd</td> <td>Character</td> <td>Cause of ESKD</td> </tr> <tr> <td>WHO_severity</td> <td>Character</td> <td>The peak (WHO) severity for the patient over the disease course</td> </tr> <tr> <td>WHO_temp_severity</td> <td>Character</td> <td>The (WHO) severity at time of sampling</td> </tr> <tr> <td>fatal_disease</td> <td>Logical</td> <td>Whether the disease was fatal</td> </tr> <tr> <td>case_control</td> <td>Character</td> <td>Whether the individual was COVID-19 <code>POSITIVE</code> or <code>NEGATIVE</code> at time of sampling. Convalescent patients are denoted by the label <code>RECOVERY</code></td> </tr> <tr> <td>radiology_evidence_covid</td> <td>Character</td> <td>Evidence of COVID-19 from radiology</td> </tr> <tr> <td>time_from_first_symptoms</td> <td>Integer</td> <td>The number of days since the individual first experienced COVID symptoms at time of sampling</td> </tr> <tr> <td>time_from_first_positive_swab</td> <td>Integer</td> <td>The number of days since the individual's first positive swab was taken at time of sampling</td> </tr> </tbody> </table>
Dataset for Earth Sciences at Freie Universität Berlin: Open Access, Licenses and Persistent Identifiers Monitoring
<p>In <em>Version 4</em>, <strong>publishers </strong>and <strong>journals</strong> names has been extended.</p> <p>In <em>Version 3</em>, new entries have been added for both <strong>journal </strong>and <strong>non-journal article outputs</strong>, specifically including data from the year <strong>2023</strong>. Minor adjustments were also made to URLs and open access (OA) statuses.</p> <p><em>Note</em>: Data for journal and non-journal article outputs from the year 2023 were unavailable at the time of preparing the <strong>short paper</strong> presenting the results, findable under <a href="https://doi.org/10.5281/zenodo.14170751" target="_blank" rel="noopener">10.5281/zenodo.14170751</a> [1]).</p> <p><br>Started in 2021, Berlin University Alliance (BUA) Open Science Dashboards, followed by the BUA Open Science Magnifiers projects, seek to investigate Open Science (OS) practices across different research domains and communities. A primary focus of these initiatives lies in the development of OS indicators, tailored to discipline specific ones, alongside their visualisation for monitoring.</p> <p>Collaborating closely with the Department of Earth Sciences at Freie Universität Berlin (FU), one of the project's key objectives is the implementation of an Open Science Dashboard for Earth Sciences FU. The visualisation of the first OS metrics is already available under <a href="https://quest-open-earthsciences.charite.de/">https://quest-open-earthsciences.charite.de/</a>.</p> <p>The datasets utilized include the outputs from the Department of Earth Sciences at FU, i.a. on Open Access (OA) categorisations and statuses, persistent identifiers (PIDs) and Open Licences (Creative Commons) availability, published between 2016-2023. These datasets consist of (i) <strong>"journal_articles_v3.csv"</strong> and (ii) <strong>"non_journal_articles_outputs_v3.csv"</strong>, the latter including “book”, “book chapter”, “conference paper”, “conference abstract”, and “other research outputs” (e.g. book reviews, project reports, book chapters in school books, or electronic supplementary material).</p> <p>Data for the dashboard was obtained from the FU university bibliography (<a href="https://frub-berlin.primo.exlibrisgroup.com/">https://frub-berlin.primo.exlibrisgroup.com/</a>), but coverage of PID information was incomplete, OA category information was incomplete and often erroneous, and copyright/open licence information was missing in this data set. Therefore, the data set was <strong>enriched with manually researched information</strong>. Data enrichment was different for journal articles and for non-journal-article publications. For <strong><em>journal articles</em></strong>, <em>copyright/open licence</em> information was added, and <em>open access category</em> information was checked and added or corrected. For <strong><em>non-journal-article outputs</em></strong>, missing <em>PIDs</em> were added and <em>open access category</em> information was checked and added or corrected. </p> <p>The "<em>data_dictionary_earth_sciences_v3.csv"</em> table documents all variables of each data file containing here.</p> <p>Both for the dashboard, and in our following publications, we categorized <strong>"bronze"</strong> OA outputs as closed access. Although such publications are openly available on the publisher's websites, they lack licence information and thus cannot be openly reused, and presumably even change its openness status at any time. Following the methodology of Charité Dashboard on Responsible Research (<a href="https://quest-dashboard.charite.de/#tabStart">https://quest-dashboard.charite.de/#tabStart</a>) we only include "gold", "hybrid" and "green" OA as true OA. Further details about the enrichment process conducted on these datasets can be found under <a href="https://doi.org/10.5281/zenodo.1099821" target="_blank" rel="noopener">10.5281/zenodo.1099821</a>9 [2]</p> <p> </p> <p>[1] Duine, M., Iarkaeva, A., & Hübner, A. (2024, November 15). Initiating discipline-specific Open Science Monitoring with the Open Science Dashboard for Earth Sciences. 28th International Conference on Science, Technology and Innovation Indicators (STI2024), Berlin, Germany. <a href="https://doi.org/10.5281/zenodo.14170751" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.14170751</a><br>[2] Duine, M., Hübner, A., & Iarkaeva, A. (2024). Enrichment of university bibliography data for open science monitoring. Zenodo. <a href="https://doi.org/10.5281/zenodo.10998219">https://doi.org/10.5281/zenodo.10998219</a></p>
Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection
<p>Macrophages mediate key antimicrobial responses against intracellular bacterial pathogens, such as <em>Salmonella enterica</em>. Yet, they can also act as a permissive niche for these pathogens to persist in infected tissues within granulomas, which are immunological structures comprised of macrophages and other immune cells. We apply single-cell transcriptomics to investigate macrophage functional diversity during persistent <em>Salmonella</em> <em>enterica</em> serovar Typhimurium (<em>S</em>Tm) infection in mice. We identify determinants of macrophage heterogeneity in infected spleens and describe populations of distinct phenotypes, functional programming, and spatial localization. Using a <em>S</em>Tm mutant with impaired ability to polarize macrophage phenotypes, we find that angiotensin converting enzyme (ACE) defines a granuloma macrophage population that is non-permissive for intracellular bacteria and their abundance anticorrelates with tissue bacterial burden. Disruption of pathogen control by neutralizing TNF is linked to preferential depletion of ACE<sup>+</sup> macrophages in infected tissues. Thus ACE<em><sup>+</sup></em> macrophages have limited capacity to serve as cellular niche for intracellular bacteria to establish persistent infection.</p>
BioNames persistent identifiers for taxonomic names and publications
<p>Linked data for taxonomic names in BioNames linked to publications of those names. Triples use terms from http://schema.org vocabulary, taxonomic names identified by Life Science Identifiers, publications identified with DOIs.</p>
Index Fungorum persistent identifiers for taxonomic names and publications
<p>Linked data for taxonomic names in Index Fungorum linked to publications of those names. Triples use terms from http://schema.org vocabulary, fungal names identified by Life Science Identifiers, publications identified with DOIs.</p>
Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection
Open the record for dataset details and reuse information.
Wikidata: Persistent identifiers as the basis for multilingual and human-machine collaboration
<p>This repository hosts a video recording of a dry-run of the PIDapalooza 2021 <a href="https://www.pidapalooza.org/schedule">https://www.pidapalooza.org/schedule</a> session</p> <p><strong>"Wikidata: Persistent identifiers as the basis for multilingual and human-machine collaboration"</strong><strong> </strong></p> <p>taking place Thursday January 28, 2021 00:00 - 00:30 UTC on Stage 1, as per <a href="https://sched.co/gD2n">https://sched.co/gD2n</a> .</p> <p>The video is also available on YouTube via <a href="https://youtu.be/g5VCr--Q1Ig">https://youtu.be/g5VCr--Q1Ig</a> .</p> <p>See <a href="https://etherpad.wikimedia.org/p/zenodo.4253308">https://etherpad.wikimedia.org/p/zenodo.4253308</a> for notes and <a href="https://github.com/Daniel-Mietchen/events/blob/master/PIDapalooza-2021.md">https://github.com/Daniel-Mietchen/events/blob/master/PIDapalooza-2021.md</a> for background on the session.</p> <p>Resources demoed in the recording:</p> <ul> <li>Wikidata: <a href="https://www.wikidata.org/wiki/Q420330">https://www.wikidata.org/wiki/Q420330</a> - persistent identifier</li> <li>Scholia: <a href="https://scholia.toolforge.org/event/Q47486859">https://scholia.toolforge.org/event/Q47486859</a> - PIDapalooza 2018 </li> <li>Ordia: <a href="https://ordia.toolforge.org/">https://ordia.toolforge.org/</a> <ul> <li><a href="https://ordia.toolforge.org/text-to-languages">https://ordia.toolforge.org/text-to-languages</a> </li> <li><a href="https://ordia.toolforge.org/text-to-lexemes">https://ordia.toolforge.org/text-to-lexemes</a> <ul> <li><a href="https://www.wikidata.org/wiki/Lexeme:L407266">https://www.wikidata.org/wiki/Lexeme:L407266</a> - biocapacity</li> </ul> </li> </ul> </li> </ul> <ul> <li>Lingua Libre: <a href="https://lingualibre.org/">https://lingualibre.org/</a> <ul> <li><a href="https://w.wiki/wBL">https://w.wiki/wBL</a> - audio recording example</li> </ul> </li> <li>Sample content: <ul> <li><a href="https://doi.org/10.3389/fcosc.2020.615419">https://doi.org/10.3389/fcosc.2020.615419</a> - Underestimating the Challenges of Avoiding a Ghastly Future</li> <li><a href="https://en.wikipedia.org/wiki/Persistent_identifier">https://en.wikipedia.org/wiki/Persistent_identifier</a> </li> </ul> </li> <li>Testing: <a href="https://www.wikidata.org/wiki/Q13406268">https://www.wikidata.org/wiki/Q13406268</a> - Wikidata Sandbox 2</li> </ul> <p>Also relevant:</p> <ul> <li><a href="https://w.wiki/hmb">https://w.wiki/hmb</a> - Items with Disease Ontology ID and MeSH Descriptor ID and optional descriptions in multiple languages</li> <li><a href="https://en.wikiquote.org/wiki/Identity">https://en.wikiquote.org/wiki/Identity</a> - quotes around "identity"</li> </ul> <ul> </ul>
Increasing persistent identifier use across Asia
<p>Recording and slides from the event <em>Increasing persistent identifier use across Asia</em>.</p> <p>Persistent identifiers (PIDs) are seen as a cornerstone of modern open research infrastructure, however their governance and adoption are not uniform across different countries and regions. This event, as part of the initial activities of the PID Alliance, sought to understand the variation in the use of PIDs, such as DOIs and ORCID IDs, across Asia and any barriers to adoption.</p> <p>The recordings include presentations and a panel discussion and all include English subtitles generated by otter.ai. Due to a technical issue, not all presentations were recorded but slides are available instead. </p>
Research Data Management - Persistent identifier (Video)
<p>Video of our latest presentation for the training seminars in Research Data Management of the FoDaKo-project: <a href="https://fodako.de/">https://fodako.de</a></p>
Panel: "Broken for All:: The case for persistent identifiers for digital cultural heritage resources AND Developer Track Session 2
<p>This video contains two sessions from Open Repositories 2021:</p> <p><strong>Panel: "Broken for All": the case for persistent identifiers for digital cultural heritage resources</strong><br> <em>Turner, Adrian (1); Holmes-Wong, Deborah (2); Rafique, Zahid (2); Kunze, John (1); Lohnash, Megan (3); McKinley, Matthew (4), Lund, <em>Allison</em> (5)</em><br> <em>1: California Digital Library; 2: University of Southern California Libraries; 3: California Revealed; 4: Omeka; 5: Metropolitan New York Library Council </em><br> Cultural heritage institutions within the United States have made significant investments in building unique digital collections, broadly disseminating them on the web and through networks such as the Digital Public Library of America (DPLA). The items within these collections are referenced and cited in a range of sources -- from Wikipedia and scholarly articles, to archival finding aids and classroom lesson plans. However, the application of persistent identifier schemes (e.g. DOI, ARK) for unique digital resources is relatively uncommon within the gallery, library, archive, and museum communities. Relatedly, many repositories and digital asset management systems (DAMS) widely used in these communities simply do not support persistent identifier schemes "out of the box." Hence, the URLs for the items are extremely fragile. If the collections are migrated to a different repository, the URLs can easily break -- impacting downstream networks, confounding researchers, and compounding the problem of link rot. This panel will discuss the critical role of persistent identifiers in digital collections management and dissemination and some of the challenges in applying them. It will feature case studies demonstrating how commonly-available licensed and open-source repositories can be adapted to support them.</p> <p><strong>Developer Track Session 2:</strong></p> <p><strong>Constructing a Repository Test Strategy Built on Docker Containers</strong><br> <em>Brady, Terrence W</em><br> <em>California Digital Library, United States of America</em><br> The Merritt Digital Preservation system comprises a dozen microservices and supporting services. Our team found that it was not cost effective to maintain and patch a fleet of servers to support a development environment. Our solution was to replace our development server environment with a stack of dockerized services. Once the stack was containerized, we discovered that we were able to create 3 variants of our development stack with different persistence strategies for database content and cloud storage. With these variants, the team has been able to support a variety of testing scenarios.<br> <br> <strong>Deploying a Serverless Application as a Docker Image</strong><br> <em>Brady, Terrence W</em><br> <em>California Digital Library, United States of America</em><br> A serverless application consists of a defined runtime (such as Ruby 2.7 or Python 3) and a package of code. This presentation will illustrate 3 types of code packages of different complexity and will describe the challenges of bundling more complicated dependencies such as binary files. In December 2020, the AWS Lambda serverless architecture began to support Docker images as a deployment package. This packaging approach makes it possible to run tests against a code package before it is deployed. This presentation will demonstrate the test and deployment process for a serverless application within the Merritt digital preservation system. Other repository teams hosting their applications on AWS may discover some useful patterns for testing and deploying serverless code to AWS Lambda.<br> <br> <strong>Live Demo: Create a Developer Workspace Challenge</strong><br> <em>Pottinger, Hardy Joseph</em><br> <em>California Digital Library, University of California, Office of the President, United States of America</em><br> Creating a developer workspace, a place in which you can write and test your code, can seem a daunting task. Sure, someone might have done it before, and they might even share their notes with you, but following those notes and arriving in the same place is like following a treasure map and expecting to get rich. There’s a better way, and I’m willing to prove it. This demo aims to show the process one goes through to craft a development environment with pretty much any tool, but will use Lando to conserve time. Lando is a way to bootstrap a useable development environment. It's built on Docker, and is like Docker-Compose, but much more transparent. It handles the boring details and helps you actually start developing with code in your favorite IDE, and all the services you need in Docker. It's all about making the life of a developer easier. It won't give you an application container you can deploy, but you will develop a deeper understanding of how all the pieces fit together, and you'll have a tool which can deploy those pieces to dev/stage/prod if you wish. The audience will participate in this demo.<br> <br> <strong>Building Scalable Serverless Digital Repositories using Amplify Open-source Framework</strong><br> <em>Chen, Yinlin; Jiang, Tingting; Hunter, Lee</em><br> <em>Virginia Tech, United States of America</em><br> We develop digital repositories to disseminate different types of digital content and to promote the principles of open access. Our goal is not to provide access to information to just one individual institution or group but to anyone and everyone. With that ambitious goal in mind, how do we enable our digital repositories to have the high availability and flexible scaling capabilities necessary to face unforeseen demand? How do we utilize only the resources we need without the waste of overprovisioning resources? These are some of the most challenging issues that we face. To achieve our goals, we moved from the traditional monolithic, server-based approach to serverless cloud infrastructure. By leveraging the services that AWS provides we have been able to boost the performance of our repositories 10x compared to that of our previous implementation that was hosted in-house. Our repositories now automatically scale up and down to meet any kind of traffic demands, without our intervention. In this talk, we will demonstrate our scalable serverless digital repositories and show the opportunities to explore and reflect on the ways that repositories enable openness for all.</p>
Identifying persistent, mobile and toxic (PMT) organic compounds detected in shale gas wastewater.
<p>Supporting Information (open data) for Identifying persistent, mobile and toxic (PMT) organic compounds detected in shale gas wastewater.</p>
Data from: From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis
Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to a stagnant persistent lineage, pinpointing the Devonian as the period during which this evolutionary regime shift occurred. The late Devonian biotic crisis is potentially unique among the 'Big Five' mass extinctions in exhibiting a drop in speciation rates rather than an increase in extinction. Our study reveals eurypterids show depressed speciation rates throughout the Devonian but no abnormal peaks in extinction. Loss of morphospace occupation is random across all Paleozoic extinction events; however, differential origination during the Devonian results in a migration and subsequent stagnation of occupied morphospace. This shift appears linked to an ecological transition from euryhaline taxa to freshwater species with low morphological diversity alongside a decrease in endemism. These results demonstrate the importance of the Devonian biotic crisis in reshaping Paleozoic ecosystems.
Supplementary material 3 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Comparison of main roles and responsibilities in the two main categories of administration of a Handle-based PID scheme
IPNI persistent identifiers for taxonomic names and publications
<p>Linked data for taxonomic names in IPNI linked to publications of those names. Triples use terms from http://schema.org vocabulary, plant names identified by Life Science Identifiers, publications identified with DOIs.</p>
Identifying Prognostic Variables for Persistent Upper Limb Dysfunctions After Breast Cancer Treatment
ClinicalTrials.gov study NCT05297591. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Identifying Prognostic Variables for Persistent UL Dysfunctions After Breast Cancer Treatment -Reliability and Validity
ClinicalTrials.gov study NCT05371847. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Data from: From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis
Open the record for dataset details and reuse information.
Supplementary material 1 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
The type specimen for Holorchis Castex; a case example
Figure 3 from: Hardisty AR, Addink W, Glöckler F, Güntsch A, Islam S, Weiland C (2021) A choice of persistent identifier schemes for the Distributed System of Scientific Collections (DiSSCo). Research Ideas and Outcomes 7: e67379. https://doi.org/10.3897/rio.7.e67379
Figure 3 Governance, operations, financing and architecture (GOFA) together delivering sustainability.
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.