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253 results for “data publishing”
Data from: Beyond the print - virtual paleontology in science publishing, outreach and education
Virtual paleontology unites a variety of computational techniques and methods for the visualization and analysis of fossils. Due to their great potential and increasing availability, these methods have become immensely popular in the last decade. However, communicating the wealth of digital information and results produced by the various techniques is still exacerbated by traditional methods of publication. Transferring and processing three-dimensional information, such as interactive models or animations, into scientific publications still poses a challenge. Here, we present different methods and applications to communicate digital data in academia, outreach and education. Three-dimensional PDFs, QR codes, anaglyph stereo imaging, and rapid prototyping—methods routinely used in the engineering, entertainment, or medical industries—are outlined and evaluated for their potential in science publishing and public engagement. Although limitations remain, these are simple, mostly cost-effective, and powerful tools to create novel and innovative resources for education, public engagement, or outreach.
Data from: Quality of descriptions of treatments: a review of published randomised controlled trials
OBJECTIVES: To be useable in clinical practice, treatments studied in trials must provide sufficient information to enable clinicians and researchers to replicate. We sought to assess the completeness of treatment descriptions in published randomised controlled trials using a checklist and to determine the extent to which peer reviewers and editors comment on the quality of reporting of treatments. DESIGN: Cross-sectional study. SETTING: Trials published in the BMJ, a general medical journal. PARTICIPANTS: 51 trials published in the BMJ were independently evaluated by two raters using the checklist. Reviewers' and editors' comments were also assessed for statements on treatment descriptions. PRIMARY AND SECONDARY OUTCOME MEASURES: Proportion of trials rated as replicable (primary outcome). RESULTS: For 57% (29/51) of the papers, published treatment descriptions were not considered sufficient to allow replication. Most poorly described aspects were the actual procedures involved including the sequencing of the technique (what happened and when) and the physical or informational materials used (e.g. training materials): 53% and 43% not clear, respectively. For a third of treatments, the dose/duration of individual sessions was not clear and for a quarter the schedule (interval, frequency, duration, or timing) was not clear. Although the majority of problems were not picked up by reviewers and editors, when they were detected only about two-thirds were fixed before publication. CONCLUSIONS: Journals wanting to publish research of use to practicing health care professionals need to pay more attention to descriptions of treatments. Our checklist, may be useful for reviewers, and editors and could help ensure important details of treatments are provided before papers are in the public domain.
Data for article entitled 'Quotative uses of Polish similative demonstratives', published in Linguistics
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Supplementary Materials for article entitled 'On Italian Spatial Prepositions and Measure Phrases: Reconciling Data with Theoretical Accounts', published in Linguistics
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Raw Data and Evaluation Scripts to "Twisted plywood-like tissue formation in vitro. Does curvature do the twist?" Published by Schamberger et al. in PNASnexus 2024
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CAT, TD, ADCP data for CAT research paper to be published in Journal of Water Resource Research
<p>This file contain experiment data obtained in Huangcai reservoir, Hunan, China in September, 2020. The field experiment aimed to reconstruct multi-layer current field using three-dimensional inversion technique to visualize spatiotemporal current structure.</p>
Figure 6 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 6 - Automated creation of data paper manuscripts from Ecological Metadata Language (EML) metadata in the ARPHA Writing Tool.
Figure 5 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 5 - The metadata from the GBIF Integrated Publishing Toolkit (IPT) can be downloaded as RTF or EML files and submitted to Pensoft's journals as data paper manuscripts.
Figure 3 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 3 - The user interface of the ARPHA Writing Tool through which single or multiple specimen records from GBIF, BOLD, iDigBio and PlutoF are imported through records identifiers.
Figure 1 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 1 - Recommendation of Dryad to cite both the original article in association with which the data were published and the data themselves.
Figure 7 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 7 - Selection of the journal and "Data Paper (Biosciences)" template in the ARPHA Writing Tool.
Figure 4 from: Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431
Figure 4 - Occurrence records and taxonomic treatments (if present in the article), published in the Biodiversity Data Journal, are exported in two separate Darwin Core Archives (DwC-A) and are available for direct download or harvesting via web services.
Figure 4 from: Dumnicka E, Galas J (2017) An overview of stygobiontic invertebrates of Poland based on published data. Subterranean Biology 23: 1-18. https://doi.org/10.3897/subtbiol.23.11877
Figure 4 - Distribution of Niphargus tatrensis in various habitats in Poland; a caves b surface waters c wells d springs.
Figure 5 from: Dumnicka E, Galas J (2017) An overview of stygobiontic invertebrates of Poland based on published data. Subterranean Biology 23: 1-18. https://doi.org/10.3897/subtbiol.23.11877
Figure 5 - Number of studies performed in particular habitats (dark bar) and number of records of stygobiontic species found in them (light bar).
Figure 2 from: Dumnicka E, Galas J (2017) An overview of stygobiontic invertebrates of Poland based on published data. Subterranean Biology 23: 1-18. https://doi.org/10.3897/subtbiol.23.11877
Figure 2 - Regions of Poland studied by various authors: 1 Beskid Wschodni Mts. 2 Bieszczady Mts. 3 Beskid Niski Mts. 4 Pieniny Mts. 5 Tatra Mts. 6 Orava-Podhale Depression 7 Gorce Mts. 8 Beskid Wyspowy Mts. 9 Wieliczka Foothill 10 Range of Babia Góra 11 Beskid Żywiecki Mts. 12 Beskid Mały Mts. 13 Beskid Śląski Mts. 14 Silesian Foothill 15 Sudety Mts. 16 Kłodzko Basin 17 Wałbrzych Mts. 18 Małopolska Gap of the Vistula 19 Świętokrzyskie Mts. 20 Jędrzejów Plateau 21 Kraków- Częstochowa Upland 22 Oświęcim Basin 23 Łask Upland 24 Legnica Plain 25 Poznań Lakeland 26 Vistula catchment up to Kazimierz Dolny town 27 Bóbr River catchment 28 Central Oder Valley 29 Oder catchment up to the outlet of the Warta River 30 Ełk Lakeland 31 Vistula Fen Country. a area of species occurrence without exact localization given b geographical regions with detailed localization of species provided.
Рис. 2. Схема распространения и мест встречи японского ужа на российском ΔаΛьнем Востоке: 1 — места встречи Αо 1985 г. (по Λитературным Αанным); 2 — места встречи посΛе 1985 г.; 3 — «КΛючевые ΛокаΛитеты» (см. в тексте); 4 — распространение хвойноширокоΛиственных и широкоΛиственных Λесов (по: КоΛесников 1969); 5 — граница распространения манчжурской фауны (по: Куренцов 1965) Fig. 2. Distribution map and finding localities of Hebius vibakari in the Russian Far East: 1 — findings before 1985 (according to the published data); 2 — findings after 1985; 3 — Key localities (see the text of the article); 4 — distribution of coniferous/broad-leaved and broad-leaved forests (see Kolesnikov 1969); 5 — limits of the Manchurian fauna (see Kurentsov 1965) in Особенности Распространения Японского Ужа Hebius Vibakari (H. Boie, 1826) (Colubridae: Natricinae) В Российской Части Ареаλа
Рис. 2. Схема распространения и мест встречи японского ужа на российском ΔаΛьнем Востоке: 1 — места встречи Αо 1985 г. (по Λитературным Αанным); 2 — места встречи посΛе 1985 г.; 3 — «КΛючевые ΛокаΛитеты» (см. в тексте); 4 — распространение хвойноширокоΛиственных и широкоΛиственных Λесов (по: КоΛесников 1969); 5 — граница распространения манчжурской фауны (по: Куренцов 1965) Fig. 2. Distribution map and finding localities of Hebius vibakari in the Russian Far East: 1 — findings before 1985 (according to the published data); 2 — findings after 1985; 3 — Key localities (see the text of the article); 4 — distribution of coniferous/broad-leaved and broad-leaved forests (see Kolesnikov 1969); 5 — limits of the Manchurian fauna (see Kurentsov 1965)
Figure 2 from: Erwin T, Stoev P, Penev L (2018) ZooKeys anniversary: 10 years of leadership toward open-access publishing of zoological data and establishment at Pensoft of like-minded sister journals across the biodiversity spectrum. ZooKeys 770: 1-8. https://doi.org/10.3897/zookeys.770.28105
Figure 2 New taxa published in ZooKeys, registered in ZooBank (courtesy of Richard Pyle; *until 27.6.2018).
Figure 1 from: Erwin T, Stoev P, Penev L (2018) ZooKeys anniversary: 10 years of leadership toward open-access publishing of zoological data and establishment at Pensoft of like-minded sister journals across the biodiversity spectrum. ZooKeys 770: 1-8. https://doi.org/10.3897/zookeys.770.28105
Figure 1 Growth of submitted manuscripts and published articles in ZooKeys from 2008 to 2018 (*until 27.6.2018).
Figure 3 from: Erwin T, Stoev P, Penev L (2018) ZooKeys anniversary: 10 years of leadership toward open-access publishing of zoological data and establishment at Pensoft of like-minded sister journals across the biodiversity spectrum. ZooKeys 770: 1-8. https://doi.org/10.3897/zookeys.770.28105
Figure 3 Total number of ZooKeys mentions in social media and popular magazines (Altmetric, June 2018).
Figure 1 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
Figure 1 Types of collection objects. Given are the frequencies of particular objects the survey participants' institution or department holds. Other objects include soil, crystal models, historical instruments, boreholes, etc.
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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.