Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
11,177
datasets available to search
ShareScore release 0.9.0
Dataset results
11,177 results for “identify”
Sequencing data for "Identifying and tracking mobile elements..." by van Dijk et al. (2023)
<p>The dataset contains the following directories:</p> <p><strong>All_raw_MAGs</strong>: all cross-assembled MAGs per community, with a text file for their BAT annotation results. Cross-assembly was done by combining all time points. <br> <strong>Candidatus_Saccharibacterium_MAGs</strong>: identified nanobacterium MAGs from various communities. <br> <strong>Cellvibrio_MAGs</strong>: identified cellvibrio spp. across communities. <br> <strong>Cellvibrio_Plasmids:</strong> Cp plasmids belonging to Cellvibrio (C1) which transferred from communities 8 to 4, 6, 9, and 10 (in horizontal communities)<br> <strong>Interactive_Dataset:</strong> HTML5 (Plotly) graphs to explore all xenotypic sequences and MAG abundance plots<br> <strong>Rscript_mock_data</strong>: R script used to design the mock data for the benchmark set. </p> <p>And a single spreadsheet (<strong>Xenoseq_mastersheet.xlsx, </strong>Supplementary Table 1) of data discussed in the main text.</p>
BridgeDb Complex Identifier Mapping Database
<p>BridgeDb identifier mapping databases for complexes extracted from Wikidata. Code to generate the database (https://github.com/bridgedb/Wikidata2Bridgedb - ComplexIdentifiers.java). </p>
Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers
<p>This repository contains the continuation of dataset 10.5281/zenodo.7494413 and 10.5281/zenodo.7494509.</p> <p>The file tiff_stacks_masks.zip contains the IMC image stacks and single-cell masks as tiff files.</p> <p>The IHC_TMAs.zip contains the scans of the IHC stains of ZTMA25 and the QuPATH projects used to extract the single-cell data (incl. the single-cell measurements as csv files).</p>
FIGURE4. a, b. Platynaspis lewisii Crotch; c. Platynaspis stictica Crotch; d. Platynaspis trimaculata Weise (identified material from BMNH). in A review of Platynaspini (Coleoptera: Coccinellidae) of the Indian subcontinent, including description of a new genus from north-eastern India and Bangladesh
FIGURE4. a, b. Platynaspis lewisii Crotch; c. Platynaspis stictica Crotch; d. Platynaspis trimaculata Weise (identified material from BMNH).
Shallow Slow Slip Events Identified Offshore the Osa Peninsula in Southern Costa Rica from GNSS Time Series
<p>Using new continuous GNSS time series from the region, we identify 5 distinct shallow SSEs that occurred immediately offshore and beneath the Osa peninsula: an event detected by one site in 2013, and two events occurring in close succession in both 2018 and 2022 detected by multiple stations, indicating a preliminary recurrence interval of ~4-5 years. While SSEs have been observed to the north at Nicoya, this is their first documentation in southern Costa Rica. Modeled slip distributions of the 2018 and 2022 events indicate that they ruptured the same or overlapping patches of the plate interface, nearly at the trench, updip of historic earthquakes including the 1983 Mw 7.4 Osa event. Immediately offshore, the estimated cumulative slip from the 2018 and 2022 events is sufficient to close the slip deficit from tectonic loading over the recurrence interval, likely influencing the magnitude and spatial slip distribution of future large ruptures.</p>
Replication Package for Automatically Identifying Relations Between Self-Admitted Technical Debt Across Different Sources
<p>This dataset includes a trained weight file for identifying the relations between self-admitted technical debt items.</p>
Fig. 4.—Climatic niche overlaps A and B in Identifying regional environmental factors driving differences in climatic niche overlap in Peromyscus mice
Fig. 4.—Climatic niche overlaps A and B differed among allopatric, parapatric, and sympatric species pairs of Peromyscus mice throughout North America. Bayesian 95% highest posterior density intervals estimates showed that sympatric species pairs had higher average overlap than parapatric or allopatric pairs and that parapatric pairs had higher average overlap than allopatric pairs.
Fig. 2 in Identifying regional environmental factors driving differences in climatic niche overlap in Peromyscus mice
Fig. 2.—Species richness map derived from geographic ranges of 43 species of Peromyscus mice available in the IUCN database (NatureServe and IUCN 2018). The remaining species mostly comprise island forms with ranges too small to be visualized in this map.
Fig. 3 in Identifying regional environmental factors driving differences in climatic niche overlap in Peromyscus mice
Fig. 3.—Illustration of the relative climatic niche overlap between species pairs of North American Peromyscus mice.
Fig. 1.—A in Identifying regional environmental factors driving differences in climatic niche overlap in Peromyscus mice
Fig. 1.—A visual summary of the three distribution modes and associated scenarios of range and climatic niche overlaps between species. The blue and green colors represent two different species within a pair. In this illustration, different parts of the triangle (a mountain) will exhibit different climatic conditions. When the two species (blue and green mouse) are aligned horizontally (either on the same mountain or on separate mountains), they will experience the same climatic conditions. When one species is above the other (either on the same mountain or on separate mountains), they experience different climatic conditions.
Figure 3 in Reviewing the status and demise of the Endangered Eld's deer and identifying priority sites and conservation actions in Cambodia
Figure 3: Minimum counts of Eld's deer recorded at Ang Trapeang Thmor and Siem Pang Wildlife Sanctuary.
Figure 2 in Reviewing the status and demise of the Endangered Eld's deer and identifying priority sites and conservation actions in Cambodia
Figure 2: Distribution of Eld's deer records in Cambodia up to 2020, divided into three regions: northern, eastern and central-western Cambodia. Management area boundaries, including protected areas, districts and communes, have been used to illustrate where records have occurred, and as such does not depict the actual extent of Eld's deer in each location. Svay Leu and Kaoh Nheaek Districts and Srayang Commune overlap with protected areas, however Eld's deer were recorded outside of the protected areas so only the proportion of the district/ commune outside of protected areas is shown. The historical distribution of Eld's deer prior to 2000 was outside the scope of the review, however we included any locations with pre-2000 records that appeared within our literature review. Therefore, this map is not an accurate reflection of Eld's deer historical distribution. The white area on the map is not necessarily lacking Eld's deer, given suitable habitat, but is unsurveyed.
TA B L E 2 Identified R packages useful for taxonomic name harmonization. Square brackets indicate supplementary references in Harmonizing taxon names in biodiversity data: A review of tools, databases and best practices
TA B L E 2 Identified R packages useful for taxonomic name harmonization. Square brackets indicate supplementary references
Dataset: Architecture-based Attack Path Analysis for Identifying Potential Security Incidents
<p>Dataset for the Publication of <em>Architecture-based Attack Path Analysis for Identifying Potential Security Incidents.</em></p> <p>A description of the tooling can be found in our <a href="https://fluidtrust.github.io/attack-propagation-doc/">documentation</a>.</p>
BridgeDb: pathway identifier mapping database derived from Wikidata
<p>Release of a BridgeDb gene identifier mapping database between Wikidata and Ensembl.</p> <pre>[INFO]: Database finished. INFO: old database is Wikidata 1.0.0 (build: 20230506) INFO: new database is Wikidata 1.0.0 (build: 20230506) INFO: Number of ids in Wd (Wikidata): 153715 (unchanged) INFO: Number of ids in En (Ensembl): 153637 (unchanged) INFO: new size is 95 Mb (changed +0.0%) INFO: total number of identifiers is 307352 INFO: total number of mappings is 307430 </pre>
Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome
<p>Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by hyperandrogenemia of ovarian thecal cell origin, resulting in anovulation/oligo-ovulation and infertility. Our previous studies established that ovarian theca cells isolated and propagated from ovaries of normal ovulatory women and women with PCOS, have distinctive molecular and cellular signatures that underlie the increased androgen biosynthesis in PCOS. To evaluate differences between gene expression in single cells from passaged cultures of theca cells from ovaries of normal ovulatory women and women with PCOS, we performed single-cell RNA sequencing (scRNA-seq). Results from these studies revealed differentially expressed pathways and genes involved in the acquisition of cholesterol, the precursor of steroid hormones, and steroidogenesis. Bulk RNA-seq and microarray studies confirmed the theca cell differential gene expression profiles. The expression profiles appear to be directed largely by increased levels or activity of the transcription factors SREBF1, which regulates genes involved in cholesterol acquisition (<em>LDLR, LIPA, NPC1, CYP11A1, FDX1, FDXR)</em> and GATA6, which regulates expression of genes encoding steroidogenic enzymes (<em>CYP17A1) </em>in concert with other differentially expressed transcription factors (<em>SP1</em>, <em>NR5A2</em>). This study provides insights into the molecular mechanisms underlying the hyperandrogenemia associated with PCOS, and highlights potential targets for molecular diagnosis and therapeutic intervention.</p> <p><strong>scRNA-seq data in the form of 10x Cell Ranger files are available for the following samples:</strong></p> <p>PCOS affected - Mc03, Mc10, Mc16, Mc26, Mc27</p> <p>Normal cycling women - Mc02, Mc06, Mc31, Mc40, Mc50</p> <p>A F in the sample name indicates forskolin treatment and a C indicates untreated control samples.</p> <p> </p>
Shallow Slow Slip Events Identified Offshore the Osa Peninsula in Southern Costa Rica from GNSS Time Series
<p>Using new continuous GNSS time series from the region, we identify 5 distinct shallow SSEs that occurred immediately offshore and beneath the Osa peninsula: an event detected by one site in 2013, and two events occurring in close succession in both 2018 and 2022 detected by multiple stations, indicating a preliminary recurrence interval of ~4-5 years. While SSEs have been observed to the north at Nicoya, this is their first documentation in southern Costa Rica. Modeled slip distributions of the 2018 and 2022 events indicate that they ruptured the same or overlapping patches of the plate interface, nearly at the trench, updip of historic earthquakes including the 1983 Mw 7.4 Osa event. Immediately offshore, the estimated cumulative slip from the 2018 and 2022 events is sufficient to close the slip deficit from tectonic loading over the recurrence interval, likely influencing the magnitude and spatial slip distribution of future large ruptures.</p>
Data for "The use of a graph database is a complementary approach to a classical similarity search for identifying commercially available fragment merges"
<p>The input and output data to the filtering pipeline described in "The use of a graph database is a complementary approach to a classical similarity search for identifying commercially available fragment merges"; code available from https://github.com/oxpig/fragment_network_merges. </p>
IPNI persistent identifiers for taxonomic names and publications
<p>Linked data for taxonomic names in IPNI linked to publications of those names. Triples use terms from http://schema.org vocabulary, plant names identified by Life Science Identifiers, publications identified with DOIs.</p>
Multiomic analysis of racehorses identifies the role of gut microbial butyrate in enhancing athletic performance via the gut-muscle/mitochondrial axis
<p>Gut microbes and their metabolites play a vital role in the health and host physiology, but how specific bacterial functions contribute to the exceptional athletic performance of racehorses needs to be better understood. Here, we identify an association of gut butyrate-producing bacteria with athletic performance in racehorses. Butyrate-producing bacteria and genes related to in butyrate synthesis were significantly enriched in the racehorse gut, and the targeted metabolomic results verified this conclusion. Supplementing butyrate in mice, we demonstrated that butyrate is sufficient to increase treadmill run time performance. We also show that butyrate improves the host response to exercise, significantly reducing inflammation in the small intestine, altering muscle fibre type in skeletal muscle, and increasing muscle mitochondrial function and activity. We also reported that the role of gut microbial butyrate might be conserved in the racehorse and human athlete. Overall, our study provides novel insights into gut microbial functions and paves the way for improving athletic performance by targeted gut microbiome manipulation.Gut microbes and their metabolites play a vital role in the health and host physiology, but how specific bacterial functions contribute to the exceptional athletic performance of racehorses needs to be better understood. Here, we identify an association of gut butyrate-producing bacteria with athletic performance in racehorses. Butyrate-producing bacteria and genes related to in butyrate synthesis were significantly enriched in the racehorse gut, and the targeted metabolomic results verified this conclusion. Supplementing butyrate in mice, we demonstrated that butyrate is sufficient to increase treadmill run time performance. We also show that butyrate improves the host response to exercise, significantly reducing inflammation in the small intestine, altering muscle fibre type in skeletal muscle, and increasing muscle mitochondrial function and activity. We also reported that the role of gut microbial butyrate might be conserved in the racehorse and human athlete. Overall, our study provides novel insights into gut microbial functions and paves the way for improving athletic performance by targeted gut microbiome manipulation.</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.