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1,026 results for “Linked data”
Public funding accountability: a linked open data-based methodology for analysing the scientific productivity and influence of funded projects. Dataset
<p>Tables containing the information about the projects funded by the Spanish AEI and publications acknowledging funding from Funder Registry. Both datasets where used in our publication: <em>Public funding accountability: a linked open data-based methodology for analysing the scientific productivity and influence of funded projects</em>.</p>
Data from: Anti-predator defenses are linked with high levels of genetic differentiation in frogs
<p>Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defenses in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defense exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature > 3,000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that, given the same geographic distance, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.</p>
Output data from "Emissions leakage and economic losses could limit the effectiveness of deforestation-linked oil crop import restrictions"
<p>Contains a .dat file with queried output from scenario runs used in the paper, Yarlagadda, B., X. Zhao, G. Iyer, T. Wild, N. Hultman and J. Lamontagne, "Emissions leakage and economic losses could limit the effectiveness of deforestation-linked oil crops". This output can be run with the workflow in <a href="https://github.com/brinday/oilcrop-trade-deforestation-leakage">https://github.com/brinday/oilcrop-trade-deforestation-leakage</a> to generate the figures presented in the paper.</p>
Novel Macrophage Subpopulation Linked to CAD: raw and processed data files
<div> <p>This directory contains all single-cell datasets analyzed in the "Partitioning heritability using single-cell multi-omics identifies a novel macrophage subpopulation conveying increased genetic risk of coronary artery disease". Associated scripts are available at https://github.com/jhjiang2020/multiome_paper. </p> <p><strong>Jan 2025 updates</strong>: include the 10x Cell Ranger ARC output for the scATAC-seq assay. <em>Please note that 10x peaks were not used for downstream analyses. Instead, we trimmed the atac-seq fragments to retain the 9bp Tn5 cut sites at both ends and aggregated into one consensus bed file. We then recalled peaks using `MACS3 --qvalue 1e-5 --nomodel --shift -50 --extsize 100 --broad` (see discussion in https://github.com/stuart-lab/signac/issues/682). </em></p> <p> </p> </div>
Linking Problem Landscape Features with the Performance of Individual CMA-ES Modules - Data
<p>This repository contains the performance data used in the paper "Linking Problem Landscape Features with the Performance of Individual CMA-ES Modules".</p> <p>The configurations run are in 'dt_run_confs.csv', and each other csv-file corresponds the the AUC values of one of these configurations.</p> <p>The script used to generate the full performance data is included in 'generate.py', and the processing using IOHanalyzer is shown in 'script.R' </p>
Data from: Neuron numbers link innovativeness with both absolute and relative brain size in birds
<p>A long-standing issue in biology is whether the intelligence of animals can be predicted by absolute or relative brain size. However, progress has been hampered by an insufficient understanding of how neuron numbers shape internal brain organization and cognitive performance. Based on estimations of neuron numbers for 111 bird species, we show here that the number of neurons in the pallial telencephalon is positively associated with a major expression of intelligence: innovation propensity. The number of pallial neurons, in turn, is greater in brains that are larger in both absolute and relative terms, and positively co-varies with longer post-hatching development periods. Thus, our analyses show that neuron numbers link cognitive performance to both absolute and relative brain size through developmental adjustments. These findings help unify neuro-anatomical measures at multiple levels, reconciling contradictory views over the biological significance of brain expansion. The results also highlight the value of a life history perspective to advance our understanding of the evolutionary bases of the connections between brain and cognition.</p>
Data from: Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils
<p><span>Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH<sub>4</sub>) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH<sub>4</sub> oxidation. CH<sub>4</sub> oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur. Spatial delineation of microbial activity with respect to these key microbial and biogeochemical factors at relevant scales is experimentally challenging in inherently complex and heterogeneous natural soil matrices. This work aims to overcome this barrier by spatially linking microbial CH<sub>4 </sub>oxidation with C/N chemistry and metagenomic characteristics. This is achieved by using positron-emitting radiotracers to visualize millimeter-scale active CH<sub>4</sub> uptake areas in Arctic soils with and without diapirism. X-ray absorption spectroscopic speciation of active and inactive areas shows CH<sub>4</sub> uptake spatially associates with greater proportions of inorganic N in diapiric frost boils. Metagenomic analyses reveal <em>Ralstonia pickettii</em> associates with CH<sub>4</sub> uptake across soils along with pertinent CH<sub>4</sub> and inorganic N metabolism associated genes. This study highlights the critical relationship between CH<sub>4</sub> and N cycles in Arctic soils, with potential implications for better understanding future climate. Furthermore, our experimental framework presents a novel, widely applicable strategy for unraveling ecological relationships underlying greenhouse gas dynamics under global change.</span></p>
Linked Data Conversion using Microservices
<p>Conference talk at the LINCS 2021 conference describing the motivations, design, and development process behind the creation of the NSSI (NERVE Secure Scalable Infrastructure) data conversion platform.</p>
Data and code from: Mixed infection, risk projection and misdirection: Interactions among pathogens alter links between host resources and disease
<p>A growing body of literature links resources of hosts to their risk of infectious disease. Yet most hosts encounter multiple pathogens, and projections of disease risk based on resource availability could be fundamentally wrong if they do not account for interactions among pathogens within hosts. Here, we measured infection risk of grass hosts (<i>Avena sativa</i>) exposed to three naturally-co-occurring viruses either singly or jointly (barley and cereal yellow dwarf viruses [B/CYDVs]: CYDV-RPV, BYDV-PAV, and BYDV-SGV) along experimental gradients of nitrogen and phosphorus supply. We asked whether disease risk (i.e., infection prevalence) differed in single versus co-inoculations, and whether these differences varied with rates and ratios of nitrogen and phosphorus supply. In single inoculations, the viruses did not respond strongly to nitrogen or phosphorus. However, in co-inoculations, we detected illustrative cases of 1) resource-dependent antagonism (RPV with increasing N; possibly due to competition), 2) resource-dependent facilitation (SGV with decreasing N:P; possibly due to immunosuppression), and 3) weak or no interactions within hosts (for PAV). Together, these within-host interactions created emergent patterns for co-inoculated hosts, with both infection prevalence and viral richness increasing with the combination of low nitrogen and high phosphorus supply. We demonstrate that knowledge of multiple pathogens is essential for predicting disease risk from host resources, and that projections of risk that fail to acknowledge resource-dependent interactions within hosts could be qualitatively wrong. Expansions of theory from community ecology theory may help anticipate such relationships linking host resources to diverse pathogen communities.</p>
Microscopy data from: Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli
<p>Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in <em>Escherichia coli</em>. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in <em>E. coli</em> and other bacteria. Three replication restart pathways have been identified in <em>E. coli</em>: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the <em>priB</em> replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel <em>priB </em>interactions were discovered. Far fewer connections were found with the PriA/PriC or PriC/Rep pathways, suggesting a primacy role for the PriA/PriB pathway in <em>E. coli</em>. Targeted genetic and imaging-based experiments with <em>priB</em> and its genetic partners revealed significant double-strand DNA break (DSB) accumulation in strains with mutations in <em>dam</em>, <em>rep</em>, <em>rdgC</em>, <em>lexA</em>, or <em>polA</em>. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of <em>rdgC</em> or <em>lexA</em> mutations in Δ<em>priB</em> cells. Taken together, our results highlight roles for several genes in DSB homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in <em>E. coli</em>.</p>
Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data
<p>guided walkthrough of poster at <a href="https://doi.org/10.5281/zenodo.6821815">https://doi.org/10.5281/zenodo.6821815</a></p> <p>which provides an overview of contexts, frameworks, and models from the world of bioimage data as well as metadata and the techniques for structuring this data as Linked Data.</p> <p>You can also watch the video in the browser on the <a href="https://gerbi-gmb.de/i3dbio/i3dbio-resources/metadata-guide/">I3D:bio website</a>.</p>
Experimental data linked to publication "Process optimization and study of the co-sintering behaviour of Cu-Ni multi-material 3D structures fabricated by spark plasma sintering (SPS)"
<p>Those are all the experimental data used to produce the plots in the article</p>
Supporting data for 'A shuttling-based two-qubit logic gate for linking distant silicon quantum processors'
<p>Data supporting for paper 'A shuttling-based two-qubit logic gate for linking distant silicon quantum processors'.</p> <p>All the data are stored in the HDF5 format that can be conveniently loaded by the xarray Python package.</p>
Data for the article entitled: Linking sexual size dimorphism to trophic niche partitioning in a generalist predator
<p>Sexual size dimorphism is a common phenomenon in mammals, and researchers have been trying to demonstrate the evolutionary causes leading to sexual dimorphism. Two main hypotheses emerged: (i) the sexual selection hypothesis and (ii) the sexual competition hypothesis (also called resource partitioning hypothesis). Here, we attempted to link sexual dimorphism in fishers (Pekania pennanti (Erxleben, 1777)) with their fall diet using stable isotope profiling and body and skull measurements. We used the carcasses of 39 fishers which were caught in eastern Québec during fall 2014 by volunteer trappers as well as several potential prey items ranging from small rodents to cervids. We expected minimal niche overlap between sexes, as males should be able to exploit different prey species than females. We also expected to observe an effect of age class (adults vs. juveniles) on trophic niche. As expected, we found great evidence of sexual dimorphism in both body mass and skull measurements: males were heavier and longer than females and had a larger zygomatic and intracanine width and a longer skull. While proportions of prey in diet according to sex and age did not vary greatly, we found some evidence of niche partitioning using Layman's metrics. Indeed, females tended to have a less diversified and more similar diet compared to one another, whereas males showed more diversified and contrasted diets. Despite our limited sample size, our findings provide partial support to the sexual competition hypothesis, as the difference in body and skull size based on sex could have evolved to lessen intraspecific competition in fishers.</p>
Linked Open Data for the maritime domain
<p>Linked Data in this data set have been compiled from diverse data sources providing information about Trade and Transport locations, protected areas, surveillance data of vessels and vessel characteristics. Data have been transformed into triples according to the vesselAI ontology, using <a href="http://core.ac.uk/download/pdf/212138612.pdf">RDF-Gen</a> . All geometries are provided using <a href="http://www.opengis.net/ont/geosparql">OGC</a> terms. The vesselAI ontology documentation is available<a href="http://83.212.101.70/vesselAI_ontology.html"> here</a> .</p> <p>In a nutshell, this data set comprises data from the following sources:</p> <p>1. AIS messages of moving objects retrieved from <a href="https://ais-public.kystverket.no/ais-download/">Norwegian Coastal Administration's SafeSeaNet</a> solution, combined with data provided by the <a href="http://web.ais.dk/aisdata/">Danish Maritime Authority</a>. Each record contains the coordinates of the vessel, a timestamp, an identifier for the vessel, its speed and heading. Typically, each vessel reports this information by sending an AIS message every few seconds. Each reported position is also annotated with the corresponding weather conditions according to Copernicus Climate Change Service (C3S) (files: reconstructed_traj.7z, ais202101_part1.7z, ais202101_part2.7z)</p> <p><br> . The weather variables currently considered as relative to the movement of vessels are:</p> <ul> <li> '10m_u_component_of_wind',</li> <li> '10m_v_component_of_wind',</li> <li> '2m_dewpoint_temperature',</li> <li> '2m_temperature',</li> <li> 'mean_sea_level_pressure',</li> <li> 'mean_wave_direction',</li> <li> 'mean_wave_period',</li> <li> 'precipitation_type',</li> <li> 'sea_surface_temperature',</li> <li> 'total_precipitation'</li> </ul> <p>2. Vessel characteristics retrieved from online sources, combined with information about departure and destination seaports. United Nations Code for Trade and Transport Locations (UN/LOCODE), has been also used, to annotate the seaports with their longitude, latitude and Well Known Text (WKT) information, as well as features and facilities available according to online sources (files: vesselsCharacteristics.7z, worldPorts.7z ).</p> <p>3. Regions of interest in the maritime domain include fishing areas, endangered species habitat areas, exclusive economic zones (EEZ), Natura2000 protected areas. In this snapshot we provide Natura2000 regions (file: natura2000.7z) as well as <a href="https://www.protectedplanet.net/en">World Protected Areas data set</a> (file: wdpa2022.ttl.7z )</p> <p>Updates and additional data sets can be found <a href="http://83.212.101.70/vesselAI_ontology.html">here</a> .</p> <p>The surveillance and weather data in this data set, are for January 2021 and within the region defined by the degrees:</p> <p>#west: 2.53<br> #south: 51.50<br> #north: 60.50<br> #east: 17.50</p>
Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees
<p><span>Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: </span><span>Syagrus botryophora </span><span>and S. pseudococos (Arecaceae)</span></p> <p><span>We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability.</span></p> <p><span>The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species.</span></p> <p><span>Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.</span></p>
Data from: Are genetic variation and demographic performance linked?
<p>Quantifying the empirical relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. Here, we present eight years of historical demographic data from five populations of <em>Boechera fecunda </em>(Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λ<sub>S</sub>) and extinction risk of each population. We combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, genetics and demography are not strongly correlated, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than more genetically diverse populations. Interestingly, however, a contemporary re-census revealed that, among these populations, genetic rather than demographic parameters were better predictors of current population density, with populations harboring greater genetic diversity maintaining denser populations at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of <em>B. fecunda </em>rather than alternatives such as translocations or reintroductions.</p>
Data and codes for: A link model approach to identify congestion hotspots
<p>Congestion emerges when high demand peaks put transportation systems under stress. Understanding the interplay between the spatial organization of demand, the route choices of citizens, and the underlying infrastructures is thus crucial to locate congestion hotspots and mitigate the delay. Here we develop a model where links are responsible for the processing of vehicles, which can be solved analytically before and after the onset of congestion, and provide insights into the global and local congestion. We apply our method to synthetic and real transportation networks, observing a strong agreement between the analytical solutions and the Monte Carlo simulations, and a reasonable agreement with the travel times observed in 12 cities under congested phase. Our framework can incorporate any type of routing extracted from real trajectory data to provide a more detailed description of congestion phenomena and could be used to dynamically adapt the capacity of road segments according to the flow of vehicles, or reduce congestion through hotspot pricing.</p>
Linked Open Data at cervantesvirtual.com
<p>The catalogue of the Biblioteca Virtual Miguel de Cervantes contains about 200,000 records which were originally created in compliance with the MARC21 standard. The entries in the catalogue have been recently migrated to a new relational database whose data model adheres to the conceptual models promoted by the International Federation of Library Associations and Institutions (IFLA), in particular, to the FRBR and FRAD specifications.</p> <p>The database content has been later mapped, by means of an automated procedure, to RDF triples which employ mainly the RDA vocabulary (Resource Description and Access) to describe the entities, as well as their properties and relationships. In contrast to a direct transformation, the intermediate relational model provides tighter control over the process for example through referential integrity, and therefore enhanced validation of the output. This RDF-based semantic description of the catalogue is now accessible online.</p>
Data associated with manuscript: "Foliar flavonoids across an elevation gradient: plasticity in response to UV, and links with floral pigmentation patterning"
<p>There are two datasets provided in this excel file. The data are flavonoid abundances of Argentina anserina [=Potentilla anserina] exposed to two levels of ultraviolet light in a greenhouse. The "leaf only data" tab has the combined foliar abundances of the major classes of flavonoids detected: chalcone, flavonone, flavone, flavonol, flavon-3-ol, and proanthocyanidin. This dataset was used to analyze the effect of UV treatment and elevation on flavonoid production in leaves. The "leaf and petal matching cmpnds" is the abundance of the major flavonoid classes in leaves and petals for only the compounds that were detected in both tissue types. This dataset was used for all analyses that related leaf flavonoids with petal flavonoids and petal UV pigmentation. </p>
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.