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Supplementary material 3 from: Petersen M, Hoffmann J, Glöckler F (2019) Access to Geosciences – Ways and Means to share and publish collection data. Research Ideas and Outcomes 5: e32987. https://doi.org/10.3897/rio.5.e32987
Programm of the two-day workshop Access to Geosciences: sharing and publishing data related to paleontological, mineralogical, and petrological objects using a common data standard. Museum für Naturkunde, 29-30 May 2017
Supplementary material 2 from: Petersen M, Hoffmann J, Glöckler F (2019) Access to Geosciences – Ways and Means to share and publish collection data. Research Ideas and Outcomes 5: e32987. https://doi.org/10.3897/rio.5.e32987
Results of the survey on geoscientific collection data. Names, institutions and contact details are anonymized
DNA sequence influences hexasome orientation to regulate DNA accessibility
<p>Each .mat file contains selected traces from one or more videos from a single flow cell. The file name contains the concentration of Gal4 used in the experiment. There are 7 variables in the .mat files</p> <p>data - cell array where each element is an Nx2 matrix containing donor, acceptor pixel intensities for each frame.</p> <p>FRET - cell array where each element is a Nx1 matrix containing FRET values for each frame</p> <p>path - cell array where each element is a Nx1 matrix containing the idealized FRET value calculated from vbFRET</p> <p>path2D - cell array where each element is an Nx2 matrix containing idealized intensities for donor and acceptor from vbFRET (not used)</p> <p>thigh - high fret state dwell times</p> <p>tlow - low fret state dwell times. </p> <p>We also include a matlab progam, TracesView2, that can be used to scroll through the traces.</p>
ACCESSING Main Study
<p>The uploaded tables contain the data underlying the analysis presented in the manuscript "Characterization of Human Papillomavirus prevalence and risk factors to guide cervical cancer screening in the North Tongu District, Ghana".</p>
Charles University SIS Access Log Dataset
<p>The package contains an anonymized server log collected on a live installation of a student information system run by <a href="http://www.cuni.cz">Charles University</a> between May and November 2018. The log is provided as an example of a real-life website workload, to be used in computer science research that may require realistic workload samples for experimental evaluation.</p>
Securing Access and the Future of Collections
<p>Audio from <em>Session 11: Securing Access and the Future of Collections</em>, held Friday 28 June 2019 at the LIBER 2019 Annual Conference.</p> <p>Talks included:</p> <ul> <li>11.1 <a href="https://doi.org/10.5281/zenodo.3260203">Sale and Disposal of Collections: Evidence-Based Decision Making and Professional Choices</a>, Kate Kelly and Mary O’Doherty, RCSI Royal College of Surgeons in Ireland, Ireland</li> <li>11.2 <a href="https://doi.org/10.5281/zenodo.3260207">Measuring the Impact of Special Collections and Archives in the Digital Age: Opportunities and Challenges</a>, Christina Kamposiori, Research Libraries UK, United Kingdom</li> <li>11.3 <a href="https://doi.org/10.5281/zenodo.3260209">Securing the Future of Collections at Senate House Library: Data-driven, Collaborative Appraisal and Accessioning for Financially Sustainable Special Collections and Archives</a>, Caroline Kimbell, University of London, United Kingdom</li> <li>11.4 <a href="https://doi.org/10.5281/zenodo.3260213">Open Science in Practice: Implementing Open Science Activity in Research Organizations</a>, Paul Ayris, UCL, United Kingdom</li> </ul>
Towards Open Access: Keeping up the Good Work
<p>Audio from <em>Session 12: Towards Open Science - Keeping up the Good Work</em>, held Friday 28 June 2019 at the LIBER 2019 Annual Conference.</p> <p>Talks included:</p> <ul> <li>12.1 <a href="https://doi.org/10.5281/zenodo.3260292">University Journals: Consolidating Institutional Repositories in a Free Open Access Publication Platform</a>, Saskia Woutersen-Windhouwer, University of Amsterdam and Leiden University Libraries, The Netherlands, Eva Méndez Rodríguez, Library and Information Sciences Department, Universidad Carlos III de Madrid, Spain, Jeroen Sondervan, Utrecht University Library, The Netherlands, Peter van Laarhoven, University of Groningen Library, The Netherlands, Frans Oort, Research Advisory Committee, University of Amsterdam, The Netherlands</li> <li>12.2 <a href="https://doi.org/10.5281/zenodo.3260294">DCU Press: Vision to Reality</a>, Ellen Breen, Dublin City University, Ireland</li> <li>12.3 <a href="https://doi.org/10.5281/zenodo.3260298">Opening up the Library: Transforming our Structures, Policies and Practices</a>. Joanna Ball, Roskilde University Library, Roskilde, Denmark, Graham Stone, Jisc Collections, United Kingdom, University of York Library, United Kingdom</li> <li>12.4 <a href="https://doi.org/10.5281/zenodo.3260301">No deal! Sweden Cancelled Agreement with Elsevier to Stand Up for Open Science</a>, Göran Hamrin and Cecilia Heyman-Widmark, KTH Royal Institute of Technology, Sweden</li> </ul>
Access to Collections and Digital Preservation
<p>Audio from <em>Session 9: Access to Collections and Digital Preservation</em>, held Thursday 27 June 2019 at the LIBER 2019 Annual Conference.</p> <p>Talks included:</p> <ul> <li> <p>9.1 <a href="https://doi.org/10.5281/zenodo.3259715">Access to Collections: an Essential Part of Research Collaborations</a>, Alex Fenlon, University of Birmingham, United Kingdom</p> </li> <li> <p>9.2 <a href="https://doi.org/10.5281/zenodo.3259719">Clear and Consistent: Copyright Assessment Framework for Libraries</a>, Fred Saunderson, National Library of Scotland, United Kingdom, Dafydd Tudur, National Library of Wales, United Kingdom</p> </li> <li> <p>9.3 <a href="https://doi.org/10.5281/zenodo.3259721">Networking with Networks: What is the Landscape for Digital Preservation Communities like?</a> Thomas Bähr and Michelle Lindlar, TIB Leibniz Information Center for Science and Technology University Library, Germany, Sabine Schrimpf, Deutsche Nationalbibliothek, Germany, Stefan Strathmann, Staats- und Universitätsbibliothek Göttingen, Germany, Monika Zarnitz, ZBW Leibniz-Information Center for Economics, Germany</p> </li> </ul>
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7). in An integrative taxonomic revision of the genus Triphosa Stephens, 1829 (Geometridae: Larentiinae) in the Middle East and Central Asia, with description of two new species
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7).
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis. in Description of the lucky Cophyla (Microhylidae, Cophylinae), a new arboreal frog from Marojejy National Park in north-eastern Madagascar
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis.
Accessibility Update Reviews Related to WCAG 2.2
<p>This dataset consists of user reviews from the Android App Store, specifically selecting those that mention app updates and their impact on digital accessibility, as well as their relation to the accessibility principles and guidelines of the Web Content Accessibility Guidelines (WCAG) version 2.2.</p>
Fig. 2. A–G, Aphaena discolor. A–B in Updating lanternflies biodiversity knowledge in Cambodia (Hemiptera: Fulgoromorpha: Fulgoridae) by optimizing field work surveys with citizen science involvement through Facebook networking and data access in FLOW website
Fig. 2. A–G, Aphaena discolor. A–B, specimen on his host-tree, Kirirom, 9.V.2015 (J. Constant). C, habitat in Kirirom, 9.V.2015 (J. Constant). D, Pursat, Cardamom, 2.I.2009 (J. Holden). E, Koh Kong, Tatai, 5.III.2012 (G. Chartier). F–G, Dichoptera sp. Chambok, 5.V.2015 (J. Constant). H, Kalidasa nigromaculata, Siem Reap, Angkor, 10.VIII.2014 (S. De Greef). I, Penthicodes atomaria tended by a cockroach, Cardamom Mts, 4.VIII.2013 (A. Anker). J, P. pulchella, Siem Reap, 18.IX.2013 (S. De Greef). K, P. variegata, Mondulkiri, O Reang District, 19.V.2015 (B. Barca). L–M, Polydictya tricolor, Siem Reap, Angkor, 1.VIII.2013 (S. De Greef). N–O, Polydictya sp., 8 km NNW Angkor, 6.XI.2013 (E. Smith).
Fig. 1 in Updating lanternflies biodiversity knowledge in Cambodia (Hemiptera: Fulgoromorpha: Fulgoridae) by optimizing field work surveys with citizen science involvement through Facebook networking and data access in FLOW website
Fig. 1. Call to collaboration to the study of Fulgoridae of Cambodia posted on Facebook on May 18th, 2015.
Fig. 3. A–B, Pyrops candelaria. A in Updating lanternflies biodiversity knowledge in Cambodia (Hemiptera: Fulgoromorpha: Fulgoridae) by optimizing field work surveys with citizen science involvement through Facebook networking and data access in FLOW website
Fig. 3. A–B, Pyrops candelaria. A, Chambok, 1.IX.2014 (S. Phauk). B, Kampong Tralach, 21.IX.2013 (O. Rodriguez). C–D, P. coelestinus, Chambok, 1.IX.2014 (S. Phauk). E, P. condorinus, Koh Kong, Tatai, 24.V.2015 (G. Chartier). F, P. ducalis, Mondulkiri, Seima Forest, 13.V.2015 (B. Barca). G–I, P. peguensis. G, Tumpor, Cardamom, 12.VIII.2009 (J. Holden). H, Chambok, 5.V.2015 (J. Constant). I, idem, biotope. J, P. spinolae, Ratanakiri, Veun Sai Siem Pang, 23.II.2015 (Marduk). K, P. viridirostris, Chambok, 7.V.2015 (J. Constant). L–N, Saiva gemmata. L, nymph, Chambok, 7 May 2015 (J. Constant). M, adult tended by a cockroach, Chambok, 7.V.2015 (J. Constant). N, Mondulkiri, Seima Forest, 13.V.2015 (B. Barca). O–Q, Zanna sp. O–P, Koh Kong, Tatai, 1.XI.2012 (G. Chartier). Q, Kampot, 21.XII.2013 (K.W. Meier-Doernberg).
Alignment of ITS sequences of Erysiphe specimens from Koelreuteria hosts, with Golovinomyces spp. as outgroup. The scientific names are followed by the respective GenBank accession number.
Open the record for dataset details and reuse information.
An open access dataset of reported Dengue outbreaks in Italy
<p><strong>Italian Dengue data</strong></p> <p><a href="https://www.epicentro.iss.it/arbovirosi/bollettini">Sito dell'Istituto Superiore di Sanità - Sistema nazionale di sorveglianza delle arbovirosi: i bollettini periodici</a></p> <p>Arboviral diseases are caused by viral agents carried by arthropod insects, such as mosquitoes, ticks and phlebotomas, through their bite or sting. Currently, more than 100 viruses associated with arboviruses have been identified that are capable of causing disorders in human health. The majority of these viruses belong to families and groups such as the <em>Togaviridae</em> (Alphavirus), the <em>Flaviridae</em> (Flavivirus) and the <em>Bunyaviridae</em> (Bunyavirus and Phlebovirus). In Italy, arboviral infections may arise from both imported and autochthonous cases and may present with diverse clinical symptoms. Surveillance of arboviruses is coordinated by the Istituto Superiore di Sanità (ISS) and, in the case of West Nile and Usutu virus surveillance, by the Istituto Zooprofilattico dell'Abruzzo e del Molise (Izs-AM), in collaboration with the Ministry of Health, which periodically publishes Surveillance and Response Plans to ensure early detection of cases and to reduce any spread as far as possible. Epidemiological surveillance is regulated by the "<a href="https://www.salute.gov.it/imgs/C_17_pubblicazioni_2947_allegato.pdf#page=8.08">National Plan for Prevention, Surveillance and Response to Arboviruses (PNA) 2020-2025</a>".</p> <p>In order to inform citizens and make the collected data available, which is only useful for communication and information purposes, the following information is made available under the CC-BY-4.0 licence</p> <p>- National evolution data<br>- Regional data<br>- Summary bulletins</p> <p><strong>Repository structure</strong><br>```<br>dengue/<br>│<br>├── */<br>│ ├── bulletins/<br>│ │ ├── Dengue_*.pdf<br>│ │ ├── ...<br>│ ├── surveillance/<br>│ │ ├── 2023/<br>│ │ │ ├── dengue-ita-*.csv<br>│ │ │ ├── dengue-ita-age-*.csv<br>│ │ │ ├── dengue-ita-location-exposure-*.csv<br>│ │ │ ├── dengue-ita-regions-*.csv<br>│ │ ├── ...<br>│ │ │ ├── ...<br>│ ├── dengue-ita-summary-cases.csv<br>│ ├── dengue-ita-summary-cases-regions.csv</p> <p>```</p> <p><strong>Data structure</strong></p> <p>- <a href="https://github.com/fbranda/dengue/blob/main/dati-andamento-dengue-italia.md">Evoulution data about Dengue Italy (IT)</a></p> <p><strong>Example of data use</strong></p> <p>Direct download (CSV): https://raw.githubusercontent.com/fbranda/dengue/main/surveillance/dengue-ita-2023.csv</p> <p>Python (requires `pandas`):<br>```python<br>import pandas as pd<br>df = pd.read_csv("https://raw.githubusercontent.com/fbranda/dengue/main/surveillance/dengue-ita-2023.csv")<br>```</p> <p>R (requires `httr`):<br>```r<br>library(httr)<br>df <- read.csv(text=content(GET("https://raw.githubusercontent.com/fbranda/dengue/main/surveillance/dengue-ita-2023.csv")))<br>```</p>
SRA Accessions SQLite Database
<p>This is a <strong>SQLite Database</strong> for SRA Accession IDs derived from an SRA Accessions TAB file. The database was generated using DRAmetaDBB, an <strong>experimental tool</strong> developed during <a href="http://2024.biohackathon.org">Biohackathon 2024</a>.</p> <ul> <li><strong>Database Description</strong>: This SQLite database contains SRA Accession IDs based on SRA Accession data. It is a proof of concept and part of ongoing experimental efforts to explore the potential of using SQLite to store and query SRA metadata.</li> <li><strong>Tool Used</strong>: The database was generated using a tool developed during Biohackathon 2024. This tool is still in its early stages and should be considered experimental. For more information about the tool used to generate this database, please visit the <a href="https://github.com/nishad/srameta-dbb">SRAmeta-DBB GitHub repository</a>.</li> <li><strong>Status</strong>: This database is a proof of concept and has not been thoroughly tested. It is not recommended for use in production environments or for critical applications.</li> </ul> <p>⚠️ <strong>Warning</strong><br>This database is a proof of concept created using an experimental tool. It has not been thoroughly tested, and significant changes may occur. Use it with caution, especially in any critical or production environments.</p>
FIGURE 46. Syagrus kellyana. A. Habit. B. Leaf. C. Infructescence. D. Fruit. E. Endocarp. F. Primary branch with flowers. G. Pistillate flower opened. H–I. Pistillate flowers. J–K. Staminate flowers. Drawn fresh from MBC accession 97290 in A revision of the genus Syagrus (Arecaceae)
FIGURE 46. Syagrus kellyana. A. Habit. B. Leaf. C. Infructescence. D. Fruit. E. Endocarp. F. Primary branch with flowers. G. Pistillate flower opened. H–I. Pistillate flowers. J–K. Staminate flowers. Drawn fresh from MBC accession 97290 (Noblick 5157). The scales are as follows: A–B are in meters, D–F are in decimeters and all others are in centimeters. Drawn by Wes Jurgens.
Exploring Accessibility Trends and Challenges in Mobile App Development: A Study of Stack Overflow Questions
<p>This is the dataset for the paper: Exploring Accessibility Trends and Challenges in Mobile App Development: A Study of Stack Overflow Questions</p> <p>This paper was accepted for publication at the 58th Hawaii International Conference on System Sciences (HICSS) - Software Technology Track</p> <p>Preprint: <a href="https://arxiv.org/abs/2409.07945">https://arxiv.org/abs/2409.07945</a></p>
In-Silico Mass Spectra for Compounds in the Metabolon's Annotation List (Open-Access)
<div> <p>In-silico spectra (+ve mode, M+H) were generated for Metabolon's data dictionary ( https://zenodo.org/records/10974865 ) using the ICEBERG model, re-trained using MONA/GNPS/NIST2020 spectra. </p> <p>Disclaimer: These are simulated spectra so they should be used with cautions to annotate compounds in LC-HRMS datasets. </p> <p> </p> </div>
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.