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294 results for “data discovery”
Code and Data associated with "Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations"
<p>Code and data sufficient to reproduce analyses in "Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations".</p>
Data associated with "A collaborative filtering based approach to biomedical knowledge discovery"
<p>This is the data set associated with the publication: "A collaborative filtering based approach to biomedical knowledge discovery" published in Bioinformatics.</p> <p>The data are sets of cooccurrences of biomedical terms extracted from published abstracts and full text articles. The cooccurrences are then represented in sparse matrix form. There are three different splits of this data denoted by the prefix number on the files.</p> <p>1. All - All cooccurrences combined in a single file</p> <p>2. Training/Validation - All cooccurrences in publications before 2010 in training, all novel cooccurrences in publication in 2010 go in validation</p> <p>3. Training+Validation/Test - All cooccurrences in publication upto and including 2010 in training+validation. All novel cooccurrences after 2010 in year by year increments and also all combined together</p> <p> </p> <p>Furthermore there are subset files which are used in some experiments to deal with the computational cost of evaluating the full set. The associated cuids.txt file containing a link between the row/column in the matrix with the UMLS Metathesaurus CUIDs. Hence the first row of cuids.txt matches up to the 0th row/column in the matrix. Note that the matrix is square and symmetric. This work was done with UMLS Metathesaurus 2016AB.</p>
Raw data for the SciPipe machine learning in drug discovery case study
<p>Accompanying raw data for the machine learning in drug discoverycase studies for SciPipe [1] available at https://github.com/pharmbio/scipipe-demo </p> <p>[1] http://scipipe.org</p>
Source data for "Discovery of topological Weyl fermion lines and drumhead surface states in a room temperature magnet"
<p>Source data for "Discovery of topological Weyl fermion lines and drumhead surface states in a room temperature magnet" by I. Belopolski et al., Science 365, 1278-1281 (2019).</p>
Automated discovery of reprogrammable nonlinear dynamic metamaterials — Data
<p>This dataset includes optimization and experimental data complementing the paper:</p> <p><a href="https://doi.org/10.1038/s41563-024-02008-6" target="_blank" rel="noopener">G. Bordiga, E. Medina, S. Jafarzadeh, C. Boesch, R. P. Adams, V. Tournat, K. Bertoldi. Automated discovery of reprogrammable nonlinear dynamic metamaterials. <em>Nature Materials.</em> (2024)</a>.</p> <p>Optimization and post-processing data in this dataset were generated using the code <a href="https://github.com/bertoldi-collab/DifFlexMM" target="_blank" rel="noopener">DifFlexMM</a> developed for the paper. This dataset can be loaded and visualized using <a href="https://github.com/bertoldi-collab/DifFlexMM" target="_blank" rel="noopener">DifFlexMM</a> with the following steps:</p> <ul> <li>Install <a href="https://github.com/bertoldi-collab/DifFlexMM" target="_blank" rel="noopener">DifFlexMM</a>.</li> <li>Download <code>data.zip</code> from this dataset.</li> <li>Extract <code>data.zip</code> and place its content in a <code>data</code> folder in the root of <a href="https://github.com/bertoldi-collab/DifFlexMM" target="_blank" rel="noopener">DifFlexMM</a>.</li> <li>Load the data associated with the design problems shown in the paper using the <a href="https://github.com/bertoldi-collab/DifFlexMM/tree/main/notebooks" target="_blank" rel="noopener">notebooks</a>.</li> </ul> <p>For more information on each problem, please refer to the <a href="https://github.com/bertoldi-collab/DifFlexMM" target="_blank" rel="noopener">README</a>.</p> <p>Videos illustrating the solved design problems can be viewed at <a href="https://github.com/bertoldi-collab/DifFlexMM/tree/main/videos" target="_blank" rel="noopener">DifFlexMM/videos</a>.</p>
Data from: A snow-dwelling tropical butterfly? An unprecedented discovery of a new genus of the Pedaliodes clade in an extreme, high-altitude Andean environment (Lepidoptera: Nymphalidae, Satyrinae)
<p><span><span>A new genus of satyrine butterflies, </span></span><span><span><em>Nivaliodes </em></span></span><span><span><strong>gen. nov.</strong></span></span><span><span>, is described for three species, all new – </span></span><span><span><em>N. negrobueno </em></span></span><span><span><strong>sp. nov.</strong></span></span><span><span>,</span></span><span><span><em>N. virococha</em></span></span><span> </span><span><span><strong>sp. nov.</strong></span></span><span><span> and </span></span><span><span><em>N. puriq </em></span></span><span><span><strong>sp. nov.</strong></span></span><span><span> (Lepidoptera, Nymphalidae) – with a support of molecular data and adult morphology. Target enrichment-based phylogeny indicates </span></span><span><span><em>Nivaliodes </em></span></span><span><span><strong>gen. nov.</strong></span></span><span><span> is sister to the genus </span></span><span><span><em>Pherepedaliodes</em></span></span><span><span>within an extremely diverse </span></span><span><span><em>Pedaliodes</em></span></span><span><span> clade of the predominantly Andean subtribe Pronophilina</span></span><span><span><em>. </em></span></span><span><span>Whereas an overwhelming majority of species of this group occur in tropical montane forests, </span></span><span><span><em>N. negrobueno </em></span></span><span><span><strong>sp. nov.</strong></span></span><span><span> was discovered in a central Peruvian desert puna at some 4600-4800 m asl., the highest elevation reported for any species of the Pronophilina. Individuals were observed overflying rocky slopes and resting directly on snow-covered surfaces, which is an exceptionally unusual behaviour among butterflies. The other two species of the new genus were found at lower elevations, some 3300-4200 m asl. at the timberline and in puna grassland. </span></span></p>
Data source for "A universal programmable Gaussian Boson Sampler for drug discovery"
<p>Source Data for the figures in paper.</p>
Data from: Discovery and description of a remarkable bathypelagic nudibranch, Bathydevius caudactylus, gen. et. sp. nov.
Open the record for dataset details and reuse information.
Data from: Unsupervised discovery of family specific vocal usage in the Mongolian gerbil
Open the record for dataset details and reuse information.
Data from: Leveraging data mining, active learning, and domain adaptation for efficient discovery of advanced oxygen evolution electrocatalysts
Open the record for dataset details and reuse information.
Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits. Findings: To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage PacBio long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs. Conclusions: In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products.
Data from: Ten more years of discovery: revisiting the quality of the sauropodomorph dinosaur fossil record
<p>Spatiotemporal changes in fossil specimen completeness can bias our understanding of a group's evolutionary history. The quality of the sauropodomorph fossil record was assessed a decade ago, but the number of valid species has since increased by 60%, and 17% of the taxa from that study have since undergone taxonomic revision. Here, we assess how 10 years of additional research has changed our outlook on the group's fossil record. We quantified the completeness of all 307 sauropodomorph species currently considered valid, using the skeletal completeness metric, which calculates the proportion of a complete skeleton preserved for each taxon. Taxonomic and stratigraphic age revisions, rather than new species, are the drivers of the most significant differences between the current results and those of the previous assessment. No statistical differences are found when we use our new dataset to generate temporal completeness curves based on only the taxa known in 2009 or 1999. We now observe a severe drop in mean completeness values across the Jurassic/Cretaceous boundary that never recover to pre-Cretaceous levels. Explaining this pattern is difficult, as we find no convincing evidence it is related to environmental preferences or body size changes. Instead, it might result from: (1) reduction of terrestrial fossil preservation space due to sea level rise; (2) ecological specificities and relatively high diagnosability of Cretaceous species; and/or (3) increased sampling of newly explored sites with many previously unknown taxa. Revisiting patterns in this manner allows us to test the longevity of conclusions made in previous quantitative studies.</p>
easyMF: A Web Platform for Matrix Factorization-based Biological Discovery from Large-scale Transcriptome Data
<p>With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced, but have led to challenges in extracting relevant biological knowledge hidden in the produced high-dimensional gene expression matrices. Here, we present easyMF, a user-friendly web platform that aims to facilitate biological discovery from large-scale transcriptome data through matrix factorization (MF). The easyMF platform enables users with little bioinformatics experience to streamline transcriptome analysis from raw reads to gene expression and to decompose expression matrix from thousands of genes to a handful of metagenes. easyMF also offers a series of functional modules for metagene-based exploratory analysis with an emphasis on functional gene discovery. As a modular, containerized and open-source platform, easyMF can be customized to satisfy users’ specific demands and deployed as a web server for broad applications. easyMF is freely available at https://github.com/cma2015/easyMF. We demonstrated the application of easyMF with four case studies using 940 RNA sequencing datasets from maize (<em>Zea mays </em>L<em>.</em>).</p>
Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic and reliably scored after genotyping of 105 individuals from three locations in the Eastern Atlantic Ocean. These markers will be valuable for future studies on population genetic structure assessment and for product tracing.
Data from: Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic
Background: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. Results: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. Conclusions: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia.
Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha
Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world's most important fishery species, through large-scale Sanger sequencing of expressed sequence tag (EST) regions. More than 3MB of sequence was collected in a survey of variation in more than 131KB of unique genic regions, from more than 225 separate ESTs, in a diverse ascertainment panel of 24 salmon. This survey yielded 117 TaqMan (5' nuclease) assays, almost all from separate EST regions, which were validated in population samples from 5 major stocks of salmon from the three largest basins on the Pacific coast of the coterminous United States: the Sacramento, Klamath and Columbia Rivers. The proportion of these loci that was variable in each of these stocks ranged from 86.3 to 90.6% and the mean minor allele frequency ranged from 0.194 to 0.236. There was substantial differentiation between populations with these markers, with a mean FST estimate of 0.107, and values for individual loci ranging from 0 to 0.592. This substantial polymorphism and population-specific differentiation indicates that these markers will be broadly useful, including for both pedigree reconstruction and genetic stock identification applications.
Data from: Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern
Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high-throughput DNA sequencing to discover SNPs and then developed molecular genetic assays for genotyping sets of 96 individual loci in each species. The two sets of assays were validated with multiple populations that encompass both the geographic range and the known regional genetic stocks of both species. The SNP panels developed herein accurately resolved the genetic stock structure for alewife and blueback herring that was previously identified using microsatellites and assigned individuals to regional stock of origin with high accuracy. These genetic markers, which generate data that are easily shared and combined, will greatly facilitate ongoing conservation and management of river herring including genetic assignment of marine caught individuals to stock of origin.
Data from: Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste
A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder "what good are they anyway?" and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical, and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, a hide beetle (Dermestes maculatus) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically-guided discovery of novel organisms.
Data from: First discovery of the charophycean green alga Lychnothamnus barbatus (Charophyceae) extant in the New World
Premise of the study: Although some species of Characeae, known as stoneworts, can be found on every continent except Antarctica, many species and some genera have limited geographic distributions. The genus Lychnothamnus, represented by a single extant species L. barbatus, was known only from scattered localities in Europe and Australasia until it was recently discovered in North America. Methods: Morphological identifications were made from specimens collected in Minnesota and Wisconsin, U.S.A. DNA sequences were obtained for three plastid-encoded genes (atpB, psbC, rbcL) from seven putative Lychnothamnus samples from two states in the U.S.A. Distribution and abundance were estimated in each lake using point intercept surveys where surveyors sampled aquatic vegetation. Key results: Fourteen lakes in Wisconsin and two lakes in Minnesota, U.S.A., were found to harbor Lychnothamnus barbatus. These represent the first report of this rare charophycean extant in the New World. The North American specimens matched the morphological description for L. barbatus and were compared directly with the neotype. Phylogenetic results using three plastid-encoded genes confirmed the identification placing New World samples with those from Europe and Australasia. Our phylogenetic analyses also confirmed the sister relationship between L. barbatus and Nitellopsis obtusa. Conclusions: Because this taxon is not known for aggressive invasiveness in its native range, it may have existed in heretofore-undiscovered native populations, although the possibility that it is a recent introduction cannot be eliminated. The potential for discovery of novel lineages of green algae in even well studied regions is apparently far from exhausted.
LakeBench: Benchmarks for Data Discovery over Data Lakes
<p><strong>LakeBench: Benchmarks for Data Discovery over Data Lakes</strong></p><p>Version 3 adds the wiki-join-search benchmark used in the "join search" experiments in our paper. </p><p>The data in the labels files (i.e., labels.json files or files under the labels folder) are shared under Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license: https://creativecommons.org/licenses/by-sa/4.0/</p><p>The data in the tables folder comes from different sources under various open licenses, as detailed in the README.txt file in each folder. All the datasets included in the benchmark have been verified to have a public license that allows distribution, derivatives, and commercial use.</p><p>THIS DATA IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p><p> </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.