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526 results for “OA”
Experimental validation data for in silico OA study
<p>The folder contains, ALP assay and PCR data, experimental protocols as well as scripts for plotting and analysis.</p> <p>This is related to the following git repository: https://github.com/Rapha-L/Experimental_validation_for_insilicoOA </p>
Dataset: Results of the CRAFT-OA requirement survey for OJS installation and update toolkit
<p>This dataset is the result of a CRAFT-OA survey that collected requirements for an installation and update toolkit which aims at facilitating a state-of-the-art implementation and operation of the journal software OJS. </p>
Riviste OA @ UniBo 2022-05-19
<p><strong>Scopo</strong></p> <p>Aggiornare, a distanza di 3 anni, l’analisi fatta nel 2019 su tutte le riviste pubblicate dall'Università di Bologna (elencate in <a href="https://journals.unibo.it/riviste/">https://journals.unibo.it/riviste/</a>). Abbiamo inserito i dati relativi al 2022 accanto ai dati raccolti nel 2019, per valutare quante di queste riviste:</p> <ol> <li>siano state aggiunte alla lista tra il 2019 e il 2022;</li> <li>siano effettivamente Open Access in base alla definizione di "open" introdotta dalla <a href="https://opendefinition.org/">Open Definition</a>. Per le riviste già esistenti, abbiamo rilevato l'eventuale modifica della policy open access;</li> <li>esplicitino la licenza dell’articolo nei vari formati in cui l’articolo è messo a disposizione (es. PDF e HTML), considerando soltanto gli articoli presenti nell'ultimo fascicolo pubblicato. Per le riviste già esistenti, abbiamo rilevato l'eventuale aggiunta (o eliminazione) di formati disponibili e dell'esplicita menzione della licenza in ciascuno di essi.</li> </ol> <p><strong>Dati</strong></p> <p>Il dataset allegato contiene una tabella di spreadsheet fatta con Google Docs ed esportata in CSV con i seguenti campi:</p> <ul> <li><strong>Rivista:</strong> il nome della rivista</li> <li><strong>Web:</strong> il sito web della rivista</li> <li><strong>ISSN:</strong> l’ISSN della rivista, che permette di identificarla univocamente</li> <li><strong>Dichiarato OA:</strong> specifica se la rivista si autodichiara Open Access</li> <li><strong>Licenza:</strong> il tipo di licenza associata agli articoli della rivista</li> <li><strong>OA? (2019):</strong> specifica se la licenza associata era conforme alla Open Definition nel 2019</li> <li><strong>OA? (2022):</strong> specifica se la licenza associata è conforme alla Open Definition nel 2022</li> <li><strong>Formato ultimo fascicolo (2019):</strong> i formati in cui gli articoli erano messi a disposizione nell'ultimo fascicolo pubblicato al momento della prima analisi</li> <li><strong>Formato ultimo fascicolo (2022):</strong> i formati in cui gli articoli sono messi a disposizione nell'ultimo fascicolo pubblicato ad oggi</li> <li><strong>Licenza per formato ultimo fascicolo (2019):</strong> i formati in cui la licenza era chiaramente specificata, considerando soltanto gli articoli presenti nell'ultimo fascicolo pubblicato al momento della prima analisi</li> <li><strong>Licenza per formato ultimo fascicolo (2022):</strong> i formati in cui la licenza è chiaramente specificata, considerando soltanto gli articoli presenti nell'ultimo fascicolo pubblicato ad oggi</li> <li><strong>Note (2019):</strong> eventuali note aggiunte nel 2019</li> <li><strong>Note (2022):</strong> eventuali note aggiunte in occasione della nuova analisi</li> </ul>
Riviste OA - UniBo
<p><strong>Scopo</strong></p> <p>Analizzare tutte le riviste pubblicate dall'Università di Bologna, elencate in <a href="https://journals.unibo.it/riviste/">https://journals.unibo.it/riviste/</a> per capire quante di queste:</p> <ol> <li> <p>sono effettivamente riviste Open Access in base alla definizione di "open" introdotta dalla <a href="https://opendefinition.org/">Open Definition</a>;</p> </li> <li> <p>specificano esplicitamente la licenza dell’articolo nei vari formati (es. PDF e HTML) in cui l’articolo è messo a disposizione, considerando soltanto gli articoli presenti nell'ultimo fascicolo pubblicato.</p> </li> </ol> <p><strong>Dati</strong></p> <p>Il dataset allegato contiene una tabella di spreadsheet fatta con Google Docs ed esportata in CSV con i seguenti campi:</p> <ul> <li> <p><strong>Rivista:</strong> il nome della rivista</p> </li> <li> <p><strong>Web:</strong> il sito web della rivista</p> </li> <li> <p><strong>ISSN:</strong> l’ISSN della rivista, che permette di identificarla univocamente</p> </li> <li> <p><strong>Dichiarato OA:</strong> specifica se la rivista si autodichiara Open Access</p> </li> <li> <p><strong>Licenza:</strong> il tipo di licenza associata agli articoli della rivista</p> </li> <li> <p><strong>OA?:</strong> specifica se la licenza associata è conforme alla Open Definition</p> </li> <li> <p><strong>Formato ultimo fascicolo:</strong> i formati in cui gli articoli sono messi a disposizione nell'ultimo fascicolo pubblicato</p> </li> <li> <p><strong>Licenza per formato ultimo fascicolo:</strong> i formati in cui la licenza è chiaramente specificata, considerando soltanto gli articoli presenti nell'ultimo fascicolo pubblicato</p> </li> <li> <p><strong>Note:</strong> delle note aggiuntive testuali, se necessarie</p> </li> </ul>
OA_Data_DB001
<p>The data contains a limited set of free-flight conditions, translated wind tunnel conditions as measured and corrected, and dedicated post-processed data.</p>
Forest floor weights and Oe-Oa soil depths from 9 Hillslope Project sites in Macon County, North Carolina, within the Upper Little Tennessee River Basin
Forest floor samples were collected at 9 hillslope sites representing a gradient of development, including forested, valley agriculture, and mountain housing developments in Macon County, NC. Forest floor was divided into two categories: forest floor (i.e., Oi, Oe, & Oa layers) and wood <10 cm diameter. Afterwards, the combined depth of the Oe and Oa was measured in the middle of 3 sides of the subplot. Forest floor collections were later dried and weighed before being processed for C and N analyses.
MCR LTER: Coral Reef: Conspecific aggregation mitigation of OA on calcification of the coral Pocillopora verrucosa, JEXBIO 2017
The study was conducted in April 2015 in Moorea, French Polynesia, using colonies of Pocillopora verrucosa (~ 4 cm in planar diameter) collected from the outer reef of the north shore at 10–12 m depth. Corals were collected from multiple sites separated by 100-200 m on the outer reef to maximize the likelihood that the selected coral colonies were genetically unique, and transferred directly to an acclimation tank. The experiment used a sequential design, in which corals first were incubated under 130 ambient or elevated pCO2 in flow-through tanks, and then were incubated in a recirculating flume under the same pCO2 crossed with a contrast of two colony densities (Fig. S1). Two response variables were measured in the light (calcification and net photosynthesis at a single irradiance), two response variables were measured in the dark (aerobic respiration and calcification), and two response variables were calculated from these values (gross 135 photosynthesis, and calcification integrated over 24 h). Aerobic respiration was measured as oxygen uptake, and net photosynthesis was measured as the flux of oxygen at a constant irradiance, and in both cases, oxygen uptake was given a negative notation and oxygen evolution a positive notation; gross photosynthesis was obtained by subtracting respiration from net photosynthesis. Daily calcification was calculated by integrating calcification in the 140 light over 12 h, calcification in the dark over 12 h, and summing the two values assuming each day consisted of 12 h of light at a constant intensity. The six response variables were measured for aggregates of a fixed number (n = 12) of similar-sized colonies placed in the flume in either high or low density arrays. With this design, it was not possible to measure the physiology of individual colonies in each aggregate, and therefore our results describe the 145 performance corals averaged across each aggregate. These data support the publication Evensen & Edmunds, 'Conspecific
A dataset used to determine a semantic similarity metric based on UMLS for PMC-OA
<p>We have performed a series of in-silico experiments in order to determine a semantic similarity metric based on UMLS annotations for PubMed Central Open Access. Here we have stored the data used for and obtained from such experiments. We have worked with relevant and partially relevant articles from the TREC-2005 Genomics Track Collection, from now referred as the initial collection, including a total of 4240 unique PubMed articles. From those 4240 articles, only 62 had publicly available; those 62 articles correspond to the full-text collection.</p> <p>Our data comprises flat files using tabs as separators and one Excel sheet. Tab separated values always include a first row with headings:</p> <ul> <li>Stems extracted from title and abstract for articles in the initial collection. Each row contains a stem with its inverse-document-frequency (IDF) within the initial collection. Stems were calculated following the Porter algorithm (available at http://tartarus.org/martin/PorterStemmer/java.txt) <ul> <li>stems.TA.tsv</li> </ul> </li> <li>Article profiles, i.e., terms (either word stems or UMLS concepts) found in the articles with term frequency (TF) and IDF. The first two columns correspond to PubMed Identifier (PMID) and PubMed Central identifier (PMC). PMC identifier was set to 0 whenever full-text was not available. <ul> <li>profiles.TA.tsv: Profiles according word stems in title and abstract for the initial collection</li> <li>profiles.PMID.tsv: Profiles according to UMLS concpets in title and abstract for the initial collection</li> <li>profiles.PMC_TA.tsv: Profiles according to UMLS concepts in title and abstract for the full-text collection</li> <li>profiles.PMC.tsv: Profiles according to UMLS concepts in the full-text for the full-text collection</li> </ul> </li> <li>Similarity matrixes calculated on the article profiles with PubMed Related Article metric (PMRA), BM25, and Cosine. There are matrixes for terms found in title-and-abstract as well as full-text. In a similarity matrix, a reference article (an interest has been already expressed for it) correspond to a row, while the columns correspond to all the other articles for which the similarity was calculated. <ul> <li>Matrixes for our initial collection <ul> <li>similarity.PMRA.TA.profiles.TA.tsv: Similarity matrix for profiles.TA.tsv following the algorithm PMRA. This matrix is considered the baseline for further analyses</li> <li>similarity.PMRA.profiles.PMID.tsv: Similarity matrix for profiles.PMID.tsv following the algorithm PMRA</li> <li>similarity.BM25_1.2_0.75.profiles.PMID.tsv: Similarity matrix for profiles.PMID.tsv following the algorithm BM25 with k=1.2 and b=0.75</li> <li>similarity.COSINE.profiles.PMID.tsv: Similarity matrix for profiles.PMID.tsv following the algorithm Cosine</li> </ul> </li> <li>Matrixes for our full-text collection <ul> <li>similarity.PMRA.profiles.PMC_TA.tsv: Similarity matrix for profiles.PMC_TA.tsv following the algorithm PMRA</li> <li>similarity.PMRA.profiles.PMC.tsv: Similarity matrix for profiles.PMC.tsv following the algorithm PMRA</li> <li>similarity.BM25.profiles.PMC_TA.tsv: Similarity matrix for profiles.PMC_TA.tsv following the algorithm BM25 with k=1.2 and b=0.75</li> <li>similarity.BM25.profiles.PMC.tsv: Similarity matrix for profiles.PMC.tsv following the algorithm BM25 with k= 1.2 and b= 0.75</li> <li>similarity.COSINE.profiles.PMC_TA.tsv: Similarity matrix for profiles.PMC_TA.tsv following the algorithm Cosine</li> <li>similarity.COSINE.profiles.PMC.tsv: Similarity matrix for profiles.PMC.tsv following the algorithm Cosine</li> </ul> </li> </ul> </li> <li>Correlation matrixes for similarities calculated for title-and-abstract taking as reference the similarity values obtained with PMRA for word stems on title-and-abstract. <ul> <li>pearsonCorrelation.PMRA.tsv: Correlation for similarity.PMRA.profiles.PMID.tsv</li> <li>pearsonCorrelationTopic.PMRA.tsv: Correlation for similarity.PMRA.profiles.PMID.tsv discriminated by TREC topics</li> <li>pearsonCorrelation.BM25_1.2_0.75.tsv: Correlation for similarity.BM25_1.2_0.75.profiles.PMID.tsv</li> <li>pearsonCorrelationTopic.BM25_1.2_0.75.tsv: Correlation for similarity.BM25_1.2_0.75.profiles.PMID.tsv discriminated by TREC topics</li> <li>pearsonCorrelation.COSINE.tsv: Correlation for similarity.COSINE.profiles.PMID.tsv</li> <li>pearsonCorrelationTopic.COSINE.tsv: Correlation for similarity.COSINE.profiles.PMID.tsv discriminated by TREC topics</li> </ul> </li> <li>Precision and recall summaries for the similarities calculated based on title-and-abstract. <ul> <li>StatsAllSummary.xlsx: Precision and recall at a global level, i.e., without considering TREC topics. This file includes information for BM25 with multiples values for constants k and b</li> </ul> </li> </ul> <p>Visualization for correlation matrixes as well as scattered plots for full-text based similarity is available at http://ljgarcia.github.io/semsim.benchmark</p>
Facts Extracted from EuPMC OA publications 2016-06-01 - 2016-06-05
<p>Named entities were extracted from the fulltext Open Access articles in EuropePMC by loading the text into ElasticSearch and querying with the content of the ContentMine dictionaries (http://github.com/ContentMine/dictionaries)</p>
Further analysis by ContentMine of OA Papers Returned by Querying EuropePMC with 'zika'
<p>Facts and metadata extracted from papers returned from querying EuropePMC with the phrase 'zika' using the ContentMine Cambridge pipeline. With dictionaries available at https://github.com/contentmine/dictionaries. Query and dictionaries used as of 2016-09-19.</p> <p>This dataset contains metadata and facts from 524 papers. A large number of the terms in the dictionaries used now contain wikidata IDs.</p> <p>Canary Version: 2ab2e9e7d95c2d6f81636739f383e52543befeff</p> <p>Dictionaries Version: 2498cf1bae660ae44437bcba388ef8436cc8554c</p>
Metabolomics Data Dictionary (Metabolon Inc. ) - from PMC articles (OA)
<p>A collection of metabolite and chemical names reported by Metabolon Inc. in the supplementary tables of open-access full-text articles from the PMC database.</p> <p><strong>Many entries can be duplicate because of chemical name variants reported in different articles. </strong></p>
PubMed-OA-Extraction-dataset
<p>This is the train-test-validation dataset for pubmed open-access articles keyphrase extraction task. The small_* file contains the all articles that have 5to 25 extractive keyphrases (keyphrase in the article that is inside the abstract of the article).</p>
Data from: The State of OA: A large-scale analysis of the prevalence and impact of Open Access articles
<p>This is the raw data behind the publication: </p> <p><strong>The State of OA: A large-scale analysis of the prevalence and impact of Open Access articles.</strong></p> <p>Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing the prevalence and characteristics of OA. We address this need using oaDOI, an open online service that determines OA status for 67 million articles. We use three samples, each of 100,000 articles, to investigate OA in three populations: 1) all journal articles assigned a Crossref DOI, 2) recent journal articles indexed in Web of Science, and 3) articles viewed by users of Unpaywall, an open-source browser extension that lets users find OA articles using oaDOI. We estimate that at least 28% of the scholarly literature is OA (19M in total) and that this proportion is growing, driven particularly by growth in Gold and Hybrid. The most recent year analyzed (2015) also has the highest percentage of OA (45%). Because of this growth, and the fact that readers disproportionately access newer articles, we find that Unpaywall users encounter OA quite frequently: 47% of articles they view are OA. Notably, the most common mechanism for OA is not Gold, Green, or Hybrid OA, but rather an under-discussed category we dub Bronze: articles made free-to-read on the publisher website, without an explicit Open license. We also examine the citation impact of OA articles, corroborating the so-called open-access citation advantage: accounting for age and discipline, OA articles receive 18% more citations than average, an effect driven primarily by Green and Hybrid OA. We encourage further research using the free oaDOI service, as a way to inform OA policy and practice.</p>
Fig. 1. Projection cover during vegetation period Fig. 2 in P H E N O L O G Y O F H E R B A C E O U S V Eg E Tat I O N I N Br Oa Dl Eaved Fo Res T O F K Am Sa Bo Tanic Al - Zoological Reserve
Fig. 1. Projection cover during vegetation period Fig. 2. Phenological spectrum of herbs in a) in a) 2009, b) 2010. 2009, b) 2010.
OA week 2024 Norway
<p>CC-BY https://www.openaccessweek.org/resources</p> <p> </p> <p>Photo by <a href="https://unsplash.com/photos/view-of-two-persons-hands-lyiKExA4zQA" target="_blank" rel="noopener">Austin Kehmeier</a>. Design by Kim Henze.</p>
Governing Scholar-Led OA Book Publishers: Interviews with Presses
<p>This is a set of interviews conducted by Dr. Judith Fathallah in the context of the 2023 research report "Governing Scholar-Led OA Book Publishers: Values, Practices, Barriers", with the kind assistance of the following interviewees:</p> <ul> <li> <p>François van Schalkwyk, Director of African Minds</p> </li> <li> <p>Joe Deville, Co-Founder of Mattering Press</p> </li> <li> <p>Jeff Pooley, Director of mediastudies.press</p> </li> <li> <p>Mercedes Bunz, Co-Founder of meson press</p> </li> <li> <p>Alessandra Tosi, Co-Director of Open Book Publishers</p> </li> <li> <p>Eileen Joy, Co-Director of punctum books.</p> </li> </ul> <p> </p>
MCR LTER: Coral Reef: Branches and plates of Porites rus insensitive to OA and warming. Lenz and Edmunds, JEMBE 2017
Data in support of Lenz & Edmunds, JEMBE 2017. [doi:10.1016/j.jembe.2016.10.002] This study tested the hypothesis that intraspecific morphological plasticity within a scleractinian coral elicits differential responses to elevated PCO2 and temperature. In Mo'orea, French Polynesia, two short-term laboratory experiments (21 and 14 days) were conducted to test the effects of PCO2 (400 vs. 700 µatm), and PCO2 (400 vs 1000 µatm) combined with temperature (27.0 vs. 29.8 C), on branches and plates of Porites rus. Experiments employed two irradiances (~1000 vs 200 µmol photons m-2 s-1), which characterized the microenvironments on the shallow fringing reefs where branching and plating morphologies are common, respectively. Calcification of both morphologies was insensitive to PCO2, as well as the combined effects of elevated PCO2 and temperature. Mean calcification rates were faster in high light than in low light for both morphologies, and biomass was greater in plates than branches in all treatments. Together, our results suggest P. rus is robust to increased PCO2 and high temperature within the constraints of the treatments applied. Morphological plasticity in this species does not mediate physiological resistance to low pH and high temperature. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2020). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Publisher OA Portfolios 2.0
<p>Publisher OA Portfolios as of April 2020.</p>
Robot List OA-Statistics
<p><strong>Standard Robot Exclusion List</strong><br /> used by OA-Statistics. Compilation of some popular black-list.</p> <p><strong>Status of this document </strong></p> <p>This document represents a consensus of the german project OA-Statistik. It is not an official standard backed by a standards body, or owned by any commercial organisation. It is not enforced by anybody, and there no guarantee that all current and future robots will use it. It has also been open for discussion.</p>
Sichtbarkeit von Hochschulschriften auf OA-Repositorien
<p>Word-Dokument enthaltend die Liste der untersuchten Repositorien, die Liste der untersuchten Dokumente und die für die Untersuchung verwendeten Suchanfragen aus:</p> <p>Linhart, Alexandra S. (2015): Sichtbarkeit von OA-Hochschulschriften - Eine Untersuchung deutscher institutioneller Repositorien. In: Informationspraxis 2015</p>
ScienceDex guides
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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.