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12,662 results for “Linking”
Linking Xylem Diameter Variations with Sap Flow Measurements at Harvard Forest 2003-2006
Measurements of variation in the diameter of tree stems provide a rapid response, high resolution tool for detecting changes in water tension inside the xylem. Water movement inside the xylem is caused by changes in the water tension and theoretically, the sap flow rate should be directly proportional to the water tension gradient and, therefore, also linearly linked to the xylem diameter variations. The coefficient of proportionality describes the water conductivity and elasticity of the conducting tissue. Xylem diameter variation measurements could thus provide an alternative approach for estimating sap flow rates, but currently we lack means for calibration. On the other hand, xylem diameter variation measurements could also be used as a tool for studying xylem structure and function. If we knew both the water tension in the xylem and the sap flow rate, xylem conductivity and/or elasticity could be calculated from the slope of their relationship. In this study we measured diurnal xylem diameter variation simultaneously with sap flow rates (Granier-type thermal method) in six deciduous species (Acer rubrum L., Alnus glutinosa Miller, Betula lenta L., Fagus Sylvatica L. Quercus rubra L., and Tilia vulgaris L.) for 7-91 day periods during summers 2003, 2005 and 2006 and analyzed the relationship between these two measurements. We found that in all species xylem diameter variations and sap flow rate were linearly related in daily scale (daily average R 2 = 0.61-0.87) but there was a significant variation in the daily slopes of the linear regressions. The largest variance in the slopes, however, was found between species, which is encouraging for finding a species specific calibration method for measuring sap flow rates using xylem diameter variations. At a daily timescale, xylem diameter variation and sap flow rate were related to each other via a hysteresis loop. The slopes during the morning and afternoon did not differ statistically significantly from each other,
Linking Community Dynamics and Ecosystem Function at Harvard Forest 1996-2000
Human activities are effecting profound changes in the structure and function of natural ecosystems. A comprehensive understanding of current ecosystem dynamics and future responses to global change requires an integrated investigation of ecological processes at many levels of organization. My thesis research addressed this goal by examining interactions between community- and ecosystem-level dynamics in mixed conifer broad-leaved forests in eastern North America. I addressed the nature of canopy-seedling feedbacks in mixed forests by relating seedling regeneration patterns in contrasting stand types to understory conditions (EXPERIMENT 1), and by directly manipulating resource availability to separate the individual effects of particular resources (EXPERIMENT 2). To investigate how nitrogen deposition will influence future forest composition, I examined the impact of increased nitrogen availability on regeneration of both coniferous and broad-leaved tree species under both closed canopy (EXPERIMENT 3) and simulated gap (EXPERIMENT 4) conditions. Future changes in forest composition might then influence whole-ecosystem productivity. I used two scaling approaches (leaf-level aggregation, EXPERIMENT 5; whole-tree sap flow, EXPERIMENT 6), I examined how the dominant coniferous and broad-leaved species in mixed temperate forests differed in their contributions to canopy-level photosynthesis.
Linking river metabolism time series and aquatic vegetation biomass at 11 sites along the Klamath River, California (summer 2019)
Algae blooms in rivers are difficult to quantify due to high heterogeneity, deep and swift conditions, seasonally rapid changes, and the high amount of surveyor effort needed to document river conditions. The data presented here were used to test the extent that summer time series of daily metabolism data reflected the quantity and type of vegetation biomass in a highly productive river with variable primary producer assemblages. Two categories of data are included in this data release: 1) Daily ecosystem metabolism estimates (gross primary production, GPP, ecosystem respiration, ER, and net ecosystem production, NEP), and 2) Reach scale biomass of 3 vegetation assemblages. In addition to these data products, we include the input data used to estimate metabolism, which includes high frequency measurements of dissolved oxygen, water temperature, and light. We also included the raw data used to estimate reach scale biomass, including measurements of filamentous algal and macrophyte percent cover and field samples analyzed for ash free dry mass, which were used to scale field observations of cover to reach scale biomass estimates. Metabolism and vegetation biomass data were collected at 11 reaches along the mid and lower Klamath River, California during summer 2019.
Limno-STOICH a comprehensive database linking the elemental content of organisms with inland, aquatic habitats (2025-12-11)
The Limnology Stoichiometric Traits of Organisms In their Chemical Habitats (Limno-STOICH) contains >51,000 observations of organismal elemental content fro >3,100 rivers, lakes, wetlands, and other aquatic ecosystem sites on seven continents. The data are derived from 190+ sources including author contributed collections, novel NEON-related data, and published datasets. The database also includes extensive spatial and temporal metadata to link elemental stoichiometry with ecosystem type, trophic status, etc., and information on organismal data (body size, taxonomic classifications, stable isotope composition) and water physicochemical parameters, as available. Users are encouraged to read the associated manuscript (Corman et al.) for further information.
Topics in Research on International Relations as Clusters of Citation Links
<p>Data, scripts, and results of a memetic topic clustering of citation links in papers published 2011-2015 in the specialty of political science that is dealing with international relations </p> <p>Supplementary Information to the paper about "Topics as clusters of citation links to highly cited sources: The case of research on international relation" by Frank Havemann<em> </em>(published 2021 in the OA-journal<em> Quantitative Science Studies</em> 2 (1): 204–223). <a href="https://doi.org/10.1162/qss_a_00108">https://doi.org/10.1162/qss_a_00108</a></p>
Facial and body colouration is linked to social rank in the African cichlid Astatotilapia burtoni
<p>These are raw data files for our publication studying animal colouration and behaviour in an African cichlid, <em>Astatotilapia burtoni</em>. </p> <p> </p> <p>Abstract<br>Animal colouration is important for social communication within conspecifics to signal threats to competitors or fitness to possible mates. Social status and animal colouration are covarying traits that are plastic in response to dynamic environments. In the African cichlid, Astatotilapia burtoni, body colouration and behaviour have been reported to vary with social rank. However, the nature of the interaction between these two traits is poorly understood. We hypothesise that colouration patterns could be linked to the behavioural repertoires underlying social status and situated across regions of interest on the cichlid body plan. To test this hypothesis, we generated Territorial and Non-territorial males and employed computer vision tools to quantify and visualise patterns/colour enrichment associated with stereotyped Territorial/Non-Territorial male behaviour. We report colour-behaviour interactions localised in specific areas of the body and face for two colour morphs, illustrating a more nuanced view of social behaviour and colouration. Since behavioural and morphological variation are key drivers of selection in the East African Great Rift Lakes, we surmise our data may be translatable to other cichlid lineages and underline the importance of trait covariance in sexual selection and male competition.</p>
Replication Materials for Disclosure Limitation and Confidentality Protection in Linked Data
<p>These are the data and derived figures as used in the chapter by Abowd, Schmutte, and Vilhuber, "Disclosure Limitation and Confidentiality Protection in Linked Data"</p>
GDPRtEXT - GDPR as a Linked Data Resource
<p>The General Data Protection Regulation (GDPR) is the new European data protection law whose compliance affects organisations in several aspects related to the use of consent and personal data. With emerging research and innovation in data management solutions claiming assistance with various provisions of the GDPR, the task of comparing the degree and scope of such solutions is a challenge without a way to consolidate them. With GDPR as a linked data resource, it is possible to link together information and approaches addressing specific articles and thereby compare them. Organisations can take advantage of this by linking queries and results directly to the relevant text, thereby making it possible to record and measure their solutions for compliance towards specific obligations. GDPR text extensions (GDPRtEXT) uses the European Legislation Identifier (ELI) ontology published by the European Publications Office for exposing the GDPR as linked data. The dataset is published using DCAT and includes an online webpage with HTML id attributes for each article and its subpoints. A SKOS vocabulary is provided that links concepts with the relevant text in GDPR.</p>
Sample data for evaluating Scholix relationship SubTypes for linked data publications
<p>Scholix links provide a standardized framework for establishing connections between research publications and their associated datasets or related data publications, thereby fostering improved discoverability, reusability, and reproducibility of research data.<br><br>This dataset aims to facilitate the evaluation of the degree of relatedness between literature publications and their associated linked data publications. It comprises 3,600 tuples, each representing a pair of a literature publication (A) and a linked data publication (B) connected through Scholix links.</p> <p><strong>Dataset Contents</strong></p> <p>1. <em>Scholix Links</em>: The dataset includes 450 Scholix links for each of the eight most frequently observed relationship types between literature and linked data publications, as expressed in the "RelationshipType - SubType" field of Scholix metadata:</p> <ul> <li>IsSupplementedBy</li> <li>IsReferencedBy</li> <li>IsRelatedTo</li> <li>References</li> <li>Documents</li> <li>Cites</li> <li>IsSupplementTo</li> <li>IsCitedBy</li> </ul> <p>2. <em>Publication Metadata</em>: In addition to the Scholix links, the dataset is augmented with metadata for each publication, including titles and author names. This metadata was harvested from the Crossref and DataCite APIs.</p> <p>3. <em>Relatedness Measures</em>: To estimate the degree of relatedness between literature and linked data publications, the dataset includes numeric measures for the similarity of authors' lists and publication titles for each tuple.</p> <p><strong>Data Sources</strong></p> <ul> <li>Scholix links were harvested from the Scholexplorer API.</li> <li>Publication metadata (titles and author names) were obtained from the Crossref and DataCite APIs.</li> </ul> <p>This dataset can be valuable for researchers and practitioners working on linked literature and data publications, evaluating the quality of existing links, or developing algorithms to identify related publications across different domains.</p>
WikiLinkGraphs: A complete, longitudinal and multilanguage dataset of the Wikipedia link networks
<p>This dataset contains yearly snapshots of the Wikipedia's internal link network for the 9 largest language edition (de, en, es, fr, it, nl, pl, ru, sv). The dataset spans over 17 years, from the creation of Wikipedia in 2001 to March 2018. The snapshots are taken on March 1st of every year.</p> <p>The graphs include the links extract from the wikitext of each page (i.e in the form [[wikilink]]). Links transcluded from templates are not included. Redirects are resolved to their target page.</p> <p>More detailed information and supporting datasets are available at: http://disi.unitn.it/~consonni/datasets/.</p> <p><strong>IMPORTANT NOTICE</strong></p> <p>Gzipped files are compressed two times by Zenodo, the MD5 provided by Zenodo and the SHA512 sums provided in the `.sha512sums.txt` files, match with the files compressed once. In other words, when you download a `.gz` file save it as `.gz.gz`, uncompress it once and it should match both the MD5 provided by Zenodo and the SHA512 sum provided by us. We have opened a bug report for this behavior on Zenodo's repository at: https://github.com/zenodo/zenodo/issues/1705</p> <p> </p>
Multi-omics analysis reveals the link between Treg distribution and therapy efficacy in Hepatocellular Carcinoma patients treated with tremelimumab plus durvalumab
<p><strong><span><span>Introduction</span></span></strong></p> <p><span>Hepatocellular carcinoma (HCC) remains a significant contributor to cancer-related deaths. Immunotherapy, either alone or in combination, has emerged as the standard treatment for advanced HCC. Notably, the combination of durvalumab (dur) and tremelimumab (trem) has received FDA approval based on findings from the HIMALAYA trial. However, comprehensive studies elucidating immune responses are lacking. We conducted a thorough analysis utilizing clinical samples from tumor biopsies to understand the mechanism of response.</span></p> <p><strong><span><span>Methods</span></span></strong></p> <p><span>Multiplexed immunofluorescence microscopy was used to analyze immune cell infiltration in primary human liver cancer samples. We developed and validated a comprehensive 37-plex antibody panel for immunofluorescence imaging of human FFPE samples. We applied highly multiplexed co-detection by indexing (CODEX) technology to simultaneously profile in situ expression of 37 proteins at sub-cellular resolution in 20 HCC patient samples using whole slide scanning. We established an image analysis pipeline to quantify all major cell populations in the human liver using supervised manual gating and unsupervised clustering algorithms using the exported matrix of the marker expression and spatial information. Clinical metadata including sex, gender, ethnicity, pretreatment, and histopathological reports are available for all patient samples.</span></p> <p><strong><span><span>Results</span></span></strong></p> <p><span><span>Using high-dimensional spatially resolved quantitative analysis of multiplexed immunofluorescence microscopy images, we generated a unique dataset and profiled the single-cell pathology landscape for human HCC treated with immunotherapy. In situ phenotyping of 400,000 single cells (including 130,000 CD45+ immune cells) allowed for the quantification of cell phenotype clusters, differential analysis of activation markers, and spatial features of each individual cell. This analysis revealed the comprehensive profile of the cell composition and spatial interactions of different cells in the TiME of patients treated with immunotherapy. Further details on the study can be obtained in our paper once it’s published.</span></span></p> <p><strong><span><span>Conclusion</span></span></strong></p> <p><span><span>We developed the CODEX panel for FFPE biopsy samples of HCC patients.</span></span></p>
EuDML zbMATH Open fulltext links subset (preview version)
<p>Lists all links from zbMATH Open documents that have fulltext links and an EuDML identifier. See <a href="https://doi.org/10.5281/zenodo.8021789">10.5281/zenodo.8021788</a> for more fulltext links.</p> <p>The meaning of the fields is:</p> <ul> <li><strong>eudml_id </strong>Unique identifier from EuDML. Prefix with <code>https://eudml.org/doc/</code> to visit additional information on the article. For example, <code>116878</code> is associated with <a href="https://eudml.org/doc/116878">https://eudml.org/doc/116878</a></li> <li><strong>zbmath_id</strong> Unique identifier from zbMATH Open. Prefix with <code>https://zbmath.org/</code> to visit additional information on the article. For example, <code>5224712</code> is associated with <a href="https://zbmath.org/5224712">https://zbmath.org/5224712</a></li> <li><strong>link</strong> link to the fulltext. Note that those links are not fully reliable. We estimate a success rate of 90%</li> </ul>
Supplementary Data: Global rise in forest fire emissions linked to climate change in the extratropics
<p>Supplementary Data for the paper "Global rise in forest fire emissions linked to climate change in the extratropics" by Jones et al. (2024, <em>Science</em>).</p> <p>The records include mapped pyromes and data and code used to delineate the pyromes.</p> <h3><strong>Mapped Pyromes</strong></h3> <p>The data records include mapped pyromes in three forms:</p> <ol> <li><strong>Shapefile</strong> (Jones_etal_2024_Global_Forest_Pyromes.shp.zip). Vector features in shapefile format containing data fields <em>pyrome ID</em> and <em>pyrome name</em>. The zipped file contains .shp, .dbf, .prj, .shx files.</li> <li><strong>Lower-resolution NetCDF </strong>(Jones_etal_2024_Global_Forest_Pyromes_Qdeg.nc). NetCDF version 4 file containing gridded values of <em>pyrome ID</em> at quarter-degree resolution.</li> <li><strong>Higher-resolution NetCDF</strong> (Jones_etal_2024_Global_Forest_Pyromes_005deg.nc). NetCDF version 4 file containing gridded values of <em>pyrome ID</em> at 0.05 degree resolution.</li> </ol> <p>Shapefiles are accessible via GIS programmes such as QGIS or ArcGIS. All files .shp, .dbf, .prj, .shx files must be stored in a single directory</p> <p>NetCDF files can be access by a variety of programming languages such as Python and R. For quick visualisations and access to the data structure, we suggest using the Panoply tool https://www.giss.nasa.gov/tools/panoply/.</p> <h3><strong>Correlation Data</strong></h3> <p>The data records (Correlation_Qdeg.zip) include gridded quarter-degree correlations between forest burned area (BA) and each of the following variables:</p> <ul> <li><em><strong>Fire weather index</strong></em></li> <li><em><strong>Atmospheric instability (continuous Haines index)</strong></em></li> <li><em><strong>Lightning flash density</strong></em></li> <li><em><strong>Soil moisture</strong></em></li> <li><em><strong>Vegetation productivity (Normalised Difference Vegetation Index)</strong></em></li> <li><em><strong>Population density</strong></em></li> <li><em><strong>Cropland cover</strong></em></li> <li><em><strong>Pasture cover</strong></em></li> <li><em><strong>Road density</strong></em></li> <li><em><strong>Potential fuel loads - surface fuels</strong></em></li> <li><em><strong>Potential fuel loads - shrub fuels</strong></em></li> <li><em><strong>Potential fuel loads - canopy and ladder fuels</strong></em></li> <li><em><strong>Terrain ruggedness index</strong></em></li> <li><em><strong>Forest area density</strong></em></li> </ul> <p>The BA data derive from MODIS MCD64A1 collection 6.1 (Giglio et al., 2018). BA data for forests is masked using the MODIS MOD44B product (DiMiceli et al., 2021) with a 30% tree cover threshold. The predictor data derive from multiple sources as desribed by Jones et al. (2024). See Supplementary Methods and Materials.</p> <p>The gridded correlations data are provided in Hierarchical Data Format version 5 (.hdf5) files, zipped to Correlation_Qdeg.zip. File names describe the variables used.<em> Cropland_Pasture_Qdeg.hdf5 </em>contains data for both cropland and pasture. Each file contains layers describing the Spearman's rho (ρ) correlation coefficient and the related p-value.</p> <p>As explained and justified by Jones et al. (2024), the correlation structure used depends on the variable (see Supplementary Methods and Materials) as per the following categories:</p> <ul> <li><strong><em>Fire Weather Index, Atmospheric Instability, and Lightning Flash Density:</em></strong> Monthly correlation between forest BA and each variable across all fire season months in the period 2001-2021 at the quarter-degree resolution.</li> <li><strong><em>Soil Moisture:</em></strong> Inter-annual correlation between (i) mean soil moisture during the fire season and (ii) accumulated forest BA during the fire season at quarter-degree resolution across years 2001-2021. </li> <li><strong><em>Vegetation Productivity (NDVI):</em></strong> Inter-annual correlation between (i) mean NDVI during the prior growing season and (ii) accumulated forest BA during the fire season at quarter-degree resolution across years 2001-2021. </li> <li><strong><em>Population Density, Cropland Cover, Pasture Cover, Road Density, T</em></strong><strong><em>errain Ruggedness Index, Forest Area Density: </em></strong>Spatial correlation between mean annual forest BA and each variable across the 0.05° cells within each quarter-degree cell during 2001-2021.</li> </ul> <p>Note that these grids are provided for insights into spatial variation in the input correlation data. Pyromes are defined based on correlations fitted on the spatial scale of Olson ecoregions, not quarter-degree grid cells (see further details below).</p> <h3><strong>Clustering Code</strong></h3> <p>DEMO_Clustering.zip contains R Statistics code for clustering forest ecoregions into pyromes based on correlations observed between forest BA and 14 predictors at regional level. The <em>Input</em> directory contains a .RData data frame with correlations between forest BA and each predictor for ecoregions. For demonstrative purposes the code is applied to cluster forest ecorgions of North America into pyromes. The <em>Regions</em> directory contains ecoregions of North America in shapefile format. The <em>Output</em> directory contains output generated by M. Jones, which can be used for validation purposes once other users have trialled the code.</p>
DATA: Linking Personality and Trust in Intelligent Virtual Assistants
<p>This dataset (n=367) investigates links between people's personality, their trust in intelligent virtual agents (e.g., Amazon's Alexa, Apple's Siri, etc.) and their affinity for technology interaction.</p>
French Entity-Linking dataset between annotated tweets collected during major crises in France and French Wikipedia corpus
<p>Most of the available datasets are not particularly adapted to our target application: geolocate natural disasters from social networks. First, social media posts are largely underrepresented in these datasets, and the only Twitter dataset lacks Entity-Linking annotations. Second, none of the datasets focuses on a crisis or natural disaster event.</p> <p>To mitigate these issues, we extracted a collection of French tweets written during earthquakes and major floods that have occurred in France in recent years. We set up Label-Studio in order to annotate these tweets. A total of 4617 tweets were annotated, including 1678 tweets posted during earthquakes and 2939 during floods. For each annotated tweet, mentions were annotated using the set of labels described earlier in the paper as well as, when possible, the target Wikipedia title.</p> <p>Named “RéSoCIO” in reference to the research project in which it was carried out, the dataset resulting from this work contains a total of 12 828 annotated mentions and 1 513 distinct Wikipedia entities. 85% of mentions were associated with a Wikipedia page and 94 % if we ignore the RISKNAT and DAMAGES labels, which are often difficult to map to an existing entity.</p> <table> <tbody> <tr> <td><strong>Labels</strong></td> <td><strong>#Mentions</strong></td> <td><strong>#Linked</strong></td> <td><strong>#Entities</strong></td> </tr> <tr> <td>PERSON</td> <td>315</td> <td>263</td> <td>136</td> </tr> <tr> <td>ORG</td> <td>863</td> <td>790</td> <td>281</td> </tr> <tr> <td>GEOLOC</td> <td>4375</td> <td>4234</td> <td>701</td> </tr> <tr> <td>TRANSPORT</td> <td>250</td> <td>203</td> <td>101</td> </tr> <tr> <td>EVENT</td> <td>35</td> <td>21</td> <td>16</td> </tr> <tr> <td>FACILITY</td> <td>129</td> <td>94</td> <td>49</td> </tr> <tr> <td>RISKNAT</td> <td>5502</td> <td>4994</td> <td>128</td> </tr> <tr> <td>DAMAGES</td> <td>1136</td> <td>121</td> <td>56</td> </tr> <tr> <td>OTHER</td> <td>223</td> <td>200</td> <td>46</td> </tr> <tr> <td><strong>Total</strong></td> <td><strong>12828</strong></td> <td><strong>1322</strong></td> <td><strong>1513</strong></td> </tr> </tbody> </table> <p>Overview of the mentions annotated in the Twitter dataset. #Mentions shows the total number of mentions per label, #Linked the number of mentions linked to an entity and #Entities the number of distinct entities per label present in the dataset.</p> <table> <tbody> <tr> <td><strong>Labels</strong></td> <td><strong>#Mentions</strong></td> <td><strong>#Linked</strong></td> <td><strong>#Entitie</strong>s</td> </tr> <tr> <td>PERSON</td> <td>1100102</td> <td>1098406</td> <td>557697</td> </tr> <tr> <td>ORG</td> <td>750925</td> <td>749504</td> <td>130394</td> </tr> <tr> <td>GEOLOC</td> <td>2729702</td> <td>2728296</td> <td>215924</td> </tr> <tr> <td>TRANSPORT</td> <td>161539</td> <td>160487</td> <td>53405</td> </tr> <tr> <td>EVENT</td> <td>798433</td> <td>798251</td> <td>86471</td> </tr> <tr> <td>FACILITY</td> <td>258835</td> <td>258513</td> <td>109867</td> </tr> <tr> <td>RISKNAT</td> <td>5502</td> <td>4994</td> <td>127</td> </tr> <tr> <td>DAMAGES</td> <td>1136</td> <td>121</td> <td>56</td> </tr> <tr> <td>OTHER</td> <td>4340621</td> <td>4339658</td> <td>682458</td> </tr> <tr> <td><strong>Total</strong></td> <td><strong>10146795</strong></td> <td><strong>10138230</strong></td> <td><strong>1836399</strong></td> </tr> </tbody> </table> <p>Overview of the mentions annotated in the full dataset. #Mentions shows the total number of mentions per label, #Linked the number of mentions linked to an entity and #Entities the number of distinct entities per label present in the dataset.</p>
Ports, Past and Present Heritage Stories (perma.cc link tabular data)
<p>A list of 281 heritage stories from the Ports, Past and Present project written in Omeka Classic using Curatescape. This tabular data is a modified output from the <a href="https://perma.cc/">perma.cc</a> folder containing a series of WARC records captured during the archiving phase of the project.</p> <p>This CSV contains only the original urls, titles, and perma.cc links of the stories. For more information including author, metadata and date of snapshot, see the WARC record and the perma.cc header above it by clicking on permalinks.</p>
Linking temporal changes in species composition and biomass in a globally distributed grassland experiment: The Nutrient Network
Global change drivers, such as anthropogenic nutrient inputs, are increasing globally. Nutrient deposition simultaneously alters plant biodiversity, species composition, and ecosystem processes like aboveground biomass production. These changes are underpinned by species extinction, colonization, and shifting relative abundance. Here, we use the Price equation to quantify and link the contributions of species that are lost, gained, or that persist to change in aboveground biomass in 59 experimental grassland sites. Under ambient (control) conditions, compositional and biomass turnover was high, and losses (i.e., local extinctions) were balanced by gains (i.e. colonization). Under fertilization, the decline in species richness resulted from increased species loss and from decreases in species gained. Biomass increase under fertilization resulted mostly from species that persist, and to a lesser extent from species gained. Drivers of ecological change can interact relatively independently with diversity, composition, and ecosystem processes and functions such as aboveground biomass due to the individual contributions of species lost, gained, or persisting.
Yearly pageviews of English Wikipedia articles with potential links to green open access scholarly articles
<p>Number of visits in 2019 for a sample of 23462 English Wikipedia articles which contain references to academic sources which have a green open access copy available but not yet used. The consultation statistics were retrieved from the Wikimedia pageviews API using the Python client (script also included). The sample was selected among articles which in April 2020 had at least one citation of an academic paper (using the "cite journal" template) for which OAbot (through Unpaywall data) had found a green open access URL to add (gratis open access, not necessarily libre open access). Data shows that the top 1 % most visited articles received 30 % of the visits: over 500 million in the year, corresponding to 1 million potential citation link clicks to distribute across all references assuming a 0.2 % click-through rate per Piccardi et al. (2020).</p>
Multi-omic approach to identify phenotypic modifiers underlying cerebral demyelination in X-linked adrenoleukodystrophy
<p>These are the data tables used to produce results in the publication:</p> <p>"Multi-omic approach to identify phenotypic modifiers underlying cerebral demyelination in X-linked adrenoleukodystrophy."<br> Phillip A. Richmond & Frans van der Kloet et al.</p> <p>Submitting to Frontiers in Cellular and Developmental Biology, 2020, Peroxisomal Special Issue. </p> <p>These tables include normalized measurements from four omics technologies, with no identifying information included. For details on processing, see the manuscript or contact:</p> <p>prichmond (at) cmmt (dot) ubc (dot) ca. </p> <p>Description of Files</p> <ul> <li>Sample mapping <ul> <li>20180314_sib_pairs.xlsx <ul> <li>Excel sheet describing family numbering, etc. used as a mapping table within the sheets below. </li> </ul> </li> </ul> </li> <li>Methylation: <ul> <li>DMRs_5_Families_ALL_0.10DB_Dec2019.csv <ul> <li>Significant methylated regions with delta beta at least 10 percent when a single family is left out</li> </ul> </li> <li>ALD_Deconvoluted_Betas_Dec2019.csv <ul> <li>All fitted betas for every subject (single CpG)</li> </ul> </li> <li>ALD_Limma_Final_Dec2019_CHR.csv <ul> <li>All fitted effects using limma modeling per CpG </li> </ul> </li> </ul> </li> <li>RNA: <ul> <li>Count_data.txt <ul> <li>The raw count table summed at the gene level using featureCounts.</li> </ul> </li> <li>Pvalues_all_23_01_2019.csv <ul> <li>All pvalues and log fold changes for the genes included in the modeling process (also with family left out)</li> </ul> </li> <li>Tmm_norm_counts_5_2_2020.csv <ul> <li>Tmm normalized RNA count data</li> </ul> </li> </ul> </li> <li>Proteomic <ul> <li>Report_Precursor_Peptides.xls <ul> <li>The proteomic data as an excel spreadsheet</li> </ul> </li> </ul> </li> <li>Pvalues_prot_13_3_2019.xlsx <ul> <li>The pvalues and log fold changes (also with family left out)</li> </ul> </li> <li>Lipids: <ul> <li>Lipid_data.csv <ul> <li>The lipid data (metabolites with missings are removed)</li> </ul> </li> <li>Pvalues_lipids.csv <ul> <li>Pvalues for the lipid data (also with family left out)</li> </ul> </li> </ul> </li> </ul> <p><br> NOTE: For use of these data files for processing and reproducing results of the manuscript, please see https://github.com/Phillip-a-richmond/ALD_Modifier_Project. </p> <p> </p>
Dataset for genes linked to gastroschisis along with bioinformatics analysis
<p>The dataset consists of records from genes linked to gastroschisis. Genes displaying statistical significance with gastroschisis (excluding those genes undergoing adjusted calculations with covariates) were selected and manually curated for further bioinformatics analysis.</p> <p>Figure 1 illustrates the systematic review of the literature search strategy and selection criteria, publishing crude (unadjusted) genes linked to gastroschisis from January 1, 1990 to August 2, 2020. </p> <p>The full list of tables is described in the file READ ME and remains available in CSV files.</p>
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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.