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.
12,662
datasets available to search
ShareScore release 0.9.0
Dataset results
12,662 results for “linking”
MS data linked to manuscript: https://doi.org/10.3390/pharmaceutics15020700
Open the record for dataset details and reuse information.
Linking satellites to genes with machine learning to estimate phytoplankton community structure from space
<p><strong>General description</strong></p> <p>The datasets presented in this repository have served in the development of a new ocean color algorithm to derive the relative cell abundance of seven phytoplankton groups (output of algorithm #1, called SOMRCA), as well as their contribution to total chlorophyll a (ChlaPG, output of algorithm #2, called SOMChlF) at the global scale using an omic-based marker: psbO. The outputs of the algorithm SOMChlF were compared to the HPLC-based definition of phytoplankton groups.</p> <p>All the details about this study are found in El Hourany, R., Pierella Karlusich, J., Zinger, L., Loisel, H., Levy, M., and Bowler, C.: Linking satellites to genes with machine learning to estimate phytoplankton community structure from space, Ocean Sci., 20, 217–239, https://doi.org/10.5194/os-20-217-2024, 2024.</p> <p>In "Tara_Oceans_psbO_dataset_Final.xlsx", it can be found the Tara Oceans' psbO metagenomic counts converted into relative cell abundance and Chlorophyll-a contribution for seven phytoplankton groups alongside satellite matchups. This dataset was used for algorithm development. In "Assets HPLC_SOMChlF.xlsx", the HPLC database was used as a comparison with Satellite-derived ChlaPG. Each data document presents a description sheet.</p> <p>In the following, the datasets used in this study are described.</p> <p><strong>Tara Oceans psbO metagenomic abundances</strong><br>The psbO gene is a single-copy gene in most eukaryotes and prokaryotes. We used psbO reads from the metagenomes generated by the Tara Oceans expedition as a proxy for phytoplankton relative cell abundance (see more details in Pierella Karlusich et al., 2023 Mol Ecol Res; https://doi.org/10.1111/1755-0998.13592).</p> <p>Among the 210 Tara Oceans stations, 145 stations sampled metagenomes in different ocean regimes from oligotrophic to eutrophic waters (Chl a from 0.01 to 10 mg m−3, median at 0.3 mg m−3) from 2009 to 2013. Seawater samples were filtered to differentiate five planktonic size fractions (0.22–3, 0.8–5, 5–20, 20–180, 180–2000 µm). <br>We retrieved the psbO read abundances from each Tara Oceans size-fractionated seawater sample from the Supplementary Material from Pierella Karlusich et al., 2023 Mol Ecol Res (https://www.ebi.ac.uk/biostudies/files/S-BSST761/psbO_mapping_against_Tara_Oceans_metagenomes.tsv).</p> <p>We used the psbO data to taxonomically differentiate seven phytoplankton groups: diatoms, dinoflagellates, green algae, haptophytes, pelagophytes, cryptophytes, and prokaryotes (cyanobacteria). The psbO read abundances of these seven groups are expressed as relative phytoplankton cell abundance (%) and their contribution to the Chlorophyll-a (Chla PG, in mg m-3). Phytoplankton that were not assigned to any of these seven groups (unclassified) represented less than 5 % of the total relative cell abundance among all size classes. To obtain a single value of relative cell abundance per station, we pooled the five size fractions into a single aggregated sample. For Chl a content estimation, we used a conversion via size-dependent weights (see formula 1 in El Hourany et al., 2024).</p> <p>There are two levels of information derived from the molecular dataset: relative abundance of psbO reads as a proxy for relative cell abundance and the fraction of Chl a that each group represents. Both types of information have different implications. Chl a is often used as a proxy for biomass, which is a relevant parameter for energy and matter fluxes (e.g., food webs, biogeochemical cycles). At the same time, cell abundance corresponds to species abundance for unicellular organisms, which is an important measure for inferring community assembly processes.<br> <br><strong>Satellite Matchups</strong><br>We used ocean color products from the GlobColour project (R2019, full archive reprocessed, 2020) to retrieve satellite matchups for the psbO-derived abundances. These products were constructed by merging data from various satellite sensors: Sea-viewing Wide Field-of-view Sensor (SeaWiFS), Moderate Resolution Imaging Spectroradiometer (MODIS), Visible Infrared Imaging Radiometer Suite (VIIRS), Medium Resolution Imaging Spectrometer (MERIS), and Ocean and Land Colour Instrument (OLCI).</p> <p>We used 16 GlobColour products as inputs to retrieve the phytoplankton community structure: chlorophyll a concentration (Chl a, product name: CHL1-AVW), remote sensing reflectances (Rrs) at 11 wavelengths (412, 443, 469, 490, 510, 531, 547, 555, 620, 645, and 670 nm), light attenuation coefficient at 490 nm (Kd490), photosynthetically available radiation (PAR), normalized fluorescence light height (NFLH), and particulate backscattering at 443 nm (bbp). These products have daily and 4 km spatiotemporal resolution. In addition, we used the Climate Change Initiative (CCI) sea surface temperature (SST) product at 4 km resolution and daily frequency distributed by the Copernicus Marine Services (CMEMS) portal.</p> <p><strong>HPLC datasets</strong><br>To compare satellite-derived phytoplankton group Chla fractions' distribution (outputs of the algorithm named SOMChlF) with more conventional DPA-based products, we compiled a global HPLC dataset regrouping 12 000 HPLC observations from several HPLC datasets between 1997 and 2014. This HPLC dataset was collocated with the SOMChlF-based ChlaPG. This dataset depicts the abundance of the pigments most widely used to identify major phytoplankton groups: fucoxanthin (Fuco), peridinin (Perid), alloxanthin (Allo), zeaxanthin (Zea), chlorophyll b (Chl b), 19-hexanoyloxyfucoxanthin (19HF), and 19-butanoyloxyfucoxanthin (19BF).</p> <p>Diagnostic pigments were used to estimate the Chl a fraction for each phytoplankton group, namely diatoms, dinoflagellates, haptophytes, green algae, cryptophytes, pelgophytes, and prokaryotes. The Chl a fraction per group is expressed by</p> <p>HPLC-based ChlaPG = Chla in-situ · DP · α / Sum (DP · α) where "α" is a coefficient associated with a diagnostic pigment (DP) for a specific PG.</p> <p>All the details are found in El Hourany, R., Pierella Karlusich, J., Zinger, L., Loisel, H., Levy, M., and Bowler, C.: Linking satellites to genes with machine learning to estimate phytoplankton community structure from space, Ocean Sci., 20, 217–239, https://doi.org/10.5194/os-20-217-2024, 2024.</p> <p> </p>
Molecular dynamics simulation trajectory data for "Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function"
<p>Trajectories and input files corresponding to entries in Supplementary Table S1.</p>
Research Artifact: 9.6 Million Links in Source Code Comments
<p>This is a research artifact for the ICSE'19 paper <strong>9.6 Million Links in Source Code Comments: Purpose, Evolution, and Decay</strong>. This artifact is a data repository including all 9,654,702 links associated with the information of languages and comment location (GitHub links including account names, repository names, commit hashes, file paths, and line numbers). The purpose of this artifact is enabling researchers to replicate our mixed-methods quantitative results of the paper, and to reuse our around 9.6 million links in source code comments for further software engineering research.</p>
Dataset and results for paper: Predicting missing links in directed networks: An investment-profit index
<p>Dataset and raw results for paper: Predicting missing links in directed networks: An investment-profit index. File "All_indices_12_dataset.mat" contains results of all 9 indices in 12 datasets. File "IP_sigma_12_dataset.mat" contains AUC and precision values when parameter sigma changes in IP index.</p>
Linking governance to a sustainable future. A study on the use of e-government service among undergraduate students in a Chinese Municipality
<p>The data describes the survey in the study.This study devotes to promoting the sustainability in smart governance field through e-government services. It seeks to understand the situation of e-government use in a special group of future generation: undergraduate students. In order to achieve this object, this research conducts a case study in Chongqing, China. Drawing upon data from a sample of 1046 respondents in 2019, the findings reveal that the way to interact with government via e-government is receiving by a wide range of undergraduate students. Additionally, the results witness a rise of social media in e-government services among young generation. Based on all these findings, it offers practical suggestions to the future development of e-government services in China. </p>
Analysis and quantification of ENSO linked changes in the tropical Atlantic cloud vertical distribution using 14 years of MODIS observations
<p>Time series of monthly means and anomolies of the cloud vertical distribution and other parameters used in this study.</p>
DataSet - Muscle structure governs joint function: linking natural variation in medial gastrocnemius structure with isokinetic plantar flexor function
<p>Experimental data used in analysis and computational model files for research study 'Muscle structure governs joint function: linking natural variation in medial gastrocnemius structure with isokinetic plantar flexor function'</p>
xLiD-Lexica: Cross-lingual Linked Data Lexica
<p>We provide <strong>cross-lingual linked data lexica called xLiD-Lexica</strong>. The data set contains the <strong>cross-lingual groundings of linked data resources from the Linked Open Data cloud as RDF data</strong>, which can be easily integrated into the LOD data sources. In addition, we created a SPARQL endpoint over ourxLiD-Lexica to allow users to easily access them using SPARQL query language. Multilingual and cross-lingual information access can be facilitated by the availability of such lexica, e.g., allowing for an easy mapping of natural language expressions in different languages to linked data resources from LOD. Many tasks in natural language processing, such as natural language generation, cross-lingual entity linking, text annotation and question answering, can benefit from our xLiD-Lexica.</p> <p>More information can be found in the <a href="http://dbis.informatik.uni-freiburg.de/content/team/faerber/papers/xLiD_LREC2014.pdf"><strong>LREC'14 paper <em>xLiD-Lexica: Cross-lingual Linked Data Lexica</em></strong></a> and on our website <strong><a href="https://km.aifb.kit.edu/sites/xlid-lexica/">https://km.aifb.kit.edu/sites/xlid-lexica/</a></strong>.</p> <p>Please cite this data set as follows (see also <a href="https://dblp.org/rec/bibtex/conf/lrec/ZhangFR14">DBLP</a>):</p> <pre><code>Lei Zhang, Michael Färber, Achim Rettinger. "xLiD-Lexica: Cross-lingual Linked Data Lexica". In: Proceedings of the 9th International Conference on Language Resources and Evaluation (LREC 2014). Reykjavik, Iceland, 2014, pp. 2101–2105.</code></pre> <p> </p> <p><strong>Example queries:</strong></p> <p>1. Retrieve all entities with surface form which contain "iPhone":</p> <pre><code class="language-sql">Select ?resource, ?label, ?probability from <http://www.xlid-lexica.org> where { ?resource <http://www.xlid-lexica.org/block> ?b1 . ?b1 <http://www.xlid-lexica.org/res#sf> ?sf . ?b1 <http://www.xlid-lexica.org/res#priorProbability> ?probability . ?sf <http://www.xlid-lexica.org/block> ?b2. ?b2 <http://www.xlid-lexica.org/sf#label> ?label . ?label bif:contains "iPhone" . } order by DESC(?probability) limit 100</code></pre> <p>2. Retrieve the top 100 resources for a given surface form ("iphone"):</p> <pre><code class="language-sql">Select ?resource, ?probability from <http://www.xlid-lexica.org> where { ?resource <http://www.xlid-lexica.org/block> ?b1 . ?b1 <http://www.xlid-lexica.org/res#sf> ?sf . ?b1 <http://www.xlid-lexica.org/res#priorProbability> ?probability . ?sf <http://www.xlid-lexica.org/block> ?b2. ?b2 <http://www.xlid-lexica.org/sf#label> "iphone"@en . } order by DESC(?probability) limit 100</code></pre> <p>3. Retrieve the top 100 resources for a given surface form ("iphone", case-insensitive):</p> <pre><code class="language-sql">Select ?resource, ?probability from <http://www.xlid-lexica.org> where { ?resource <http://www.xlid-lexica.org/block> ?b1 . ?b1 <http://www.xlid-lexica.org/res#sf> ?sf . ?b1 <http://www.xlid-lexica.org/res#priorProbability> ?probability . ?sf <http://www.xlid-lexica.org/block> ?b2. ?b2 <http://www.xlid-lexica.org/sf#label> ?surfaceform . filter(regex(?surfaceform, "^iphone$", "i")) } limit 100</code></pre> <p>4. Retrieve the top 100 surface forms per entity:</p> <pre><code class="language-sql">Select ?label ?probability from <http://www.xlid-lexica.org> where { <http://dbpedia.org/resource/IPhone_5> <http://www.xlid-lexica.org/block> ?b1. ?b1 <http://www.xlid-lexica.org/res#sf> ?sf. ?b1 <http://www.xlid-lexica.org/res#priorProbability> ?probability. ?sf <http://www.xlid-lexica.org/block> ?b2. ?b2 <http://www.xlid-lexica.org/sf#label> ?label. ?b2 <http://www.xlid-lexica.org/block#lang> "en". } order by DESC(?probability) limit 100</code></pre> <p> </p>
Fig. 9 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 9 Anatomy of C. nechadae sp. nov., Regrag Spring, 44 km S-E of Fes city (type locality). a Ctenidium, b stomach, c partial nervous system; d–e female genitalia: d pallial oviduct, e bursa copulatrix and seminal receptacle; f–g male genitalia: f head with penis, g prostate gland
Fig. 2 a in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 2 a Geographic distributions of recovered clades, b maximum likelihood phylogeny based on the combination of mitochondrial COI and 16S and nuclear 28S gene fragments. Numbers above branches, provided above the species level, represent bootstrap support values (BS; BS> 30)
Fig. 13 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 13 Anatomy of C. atlasensis sp. nov., Sidi Mimoun Spring, near Awa Lake, Ifrane (type locality). a Ctenidium, b stomach; c–d female genitalia: c pallial oviduct, d bursa copulatrix and seminal receptacle; e–f male genitalia: e head with penis, f prostate gland
Fig. 14 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 14 Shells, opercula and radulae of C. wakrimi sp. nov., Spring in Douar Assoul, near Khenifra, Middle Atlas (type locality). a–d Shells, a, b holotype MHNM 18ZTMH49, e protoconch and f detailed
Fig. 5 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 5 Anatomy of C. marocana, Lahjar Spring, Essaouira (type locality). a Ctenidium, b stomach, c partial nervous system, d–e female genitalia: d pallial oviduct, e bursa copulatrix and seminal receptacle; f–h
Fig. 12 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 12 Shells, opercula and radulae of C. atlasensis sp. nov., Sidi Mimoun Spring, near Awa Lake, Ifrane (type locality). a–d Shells, a holotype MHNM 18ZTMH47, b paratype MHNM 18ZTMH48. e Inner
Fig. 4 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 4 Shells, opercula and radulae of C. marocana, Lahjar Spring, Essaouira (ype locality). a–d Shells, e protoconch and f detailed microsculpture of protoconch, g inner and h outer sides of operculum; i–k radulae: i portion of radular ribbon, j central tooth of radula, k inner and outer marginal teeth
Fig. 3 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 3 Time calibrated tree of Corrosella species obtained with *BEAST based on the combined dataset (COI, 16S and 28S) and the normal uncorrelated relaxed clock model. Blue bars on nodes represent the
Fig. 11 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 11 Anatomy of C. mahouchii sp. nov., Tizerdiouin Spring, Timdghasse, 40 km S-E of Khenifra (type locality). a Ctenidium, b stomach, c partial nervous system; d–e female genitalia: d pallial oviduct, e bursa copulatrix and seminal receptacle; f–g male genitalia: f head with penis, g prostate gland
Fig. 8 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 8 Shells, opercula and radulae of C. nechadae sp. nov. a–c Shells, Regrag Spring, 44 km S-E of Fes city (type locality), a holotype MNCN 15.05/200122H, d shell, Tadoute Spring, 70 km N-E Fes, e protoconch and f detailed microsculpture of protoconch, Regrag Spring, 44 km S-E of
Fig. 7 in Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
Fig. 7 Anatomy of C. pallaryi. a Ctenidium, Ait Alla Spring, Middle Atlas; b stomach, Chebouka Spring near Miaami Lake, Middle Atlas; c partial nervous system, Spring near Chebouka River and Miaami Lake, Middle Atlas; d–e female genitalia, Chebouka Spring near Miaami Lake, Middle Atlas: d pallial oviduct, e bursa copulatrix and seminal receptacle, f–h male genitalia, Chebouka Spring near Miaami Lake, Middle Atlas: f head with penis, g prostate gland
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.