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.
1,133
datasets available to search
ShareScore release 0.7.1
Dataset results
1,133 results for “Copepods”
Targeted and untargeted LC-MS copepodamide datasets for marine and freshwater copepods
<p>This repository contains the datasets, analysis code and output generated and used in the scientific article titled "Mass spectroscopy reveals compositional differences in copepodamides from limnic and marine copepods" published in Scientific Reports (https://doi.org/10.1038/s41598-024-53247-1)<em>.</em></p> <p>Detailed information about the datasets are available in the README.txt.</p> <p>The source dataset created from the sampling effort, with targeted liquid chromatography coupled mass spectrometry (LC-MS) data, taxonomic information of individual copepods, their length measurements, estimated biomass etc is available in <em><strong>Masterfile_targeted_data_final.xlsx</strong></em>.</p> <p>The source dataset for precursor LC-MS scan data is available in <em><strong>Precursor_data_Deisotoped.xlsx</strong></em>. </p> <p>The resulting analysis data frames (last sheet in each .xlsx file) are available as separate .csv files (<strong>Arnoldt_targeted_analysis_data.csv</strong> & <strong>Arnoldt_targeted_analysis_data.xlsx</strong>). These files are denoted "Supplementary Data. 2" and "Supplementary Data. 1" respectively in the main article. Data files <strong>Chromatography.csv</strong> and <strong>zooplankton_composition_bulk.csv</strong> are used to create chromatograph line plots (Figures 3a & 3b in the article) and one of the supplementary figures (S1), respectively.</p> <p>A R-markdown file (<strong>Arnoldt_R_Code</strong><em><strong>.Rmd</strong></em>) with the code to analyse and visualise all data, and its html-output file (<strong>Arnoldt_R_Code_Output</strong><em><strong>.html</strong></em>) are also available here. The markdown files uses the four csv-files described in the paragraph above to generate all analyses and figures. The output (.html) file is denoted "Supplementary Code" in the main article.</p>
First Three-dimensional Quantification of Planktic Food Chain lower levels (Copepods) for the Ross Sea region Marine Protected Area (RSRMPA), Antarctica: Using FAIR-inspired legacy data with Machine Learning, and Open Source GIS
<p>This dataset is relative to the paper entitled: "First Three-dimensional Quantification of Planktic Food Chain lower levels (Copepods) for the Ross Sea region Marine Protected Area (RSRMPA), Antarctica: Using FAIR-inspired legacy data with Machine Learning, and Open Source GIS" publishing in journal Diversity (MPDI).</p> <p>Abstract:</p> <p>Zooplankton is a fundamental group in all aquatic ecosystems located the base of the food chain. It forms a link between the lower trophic levels with secondary consumers and shows marked fluctuations of populations with environmental change, especially reacting to heating and water acidification. At sea copepod crustaceans account for app. 70% in abundance of zooplankton and are a target of monitoring activities in key areas such as the Southern Ocean. In this study we have used FAIR-inspired legacy data (dating back to the ‘80s) collected in the Ross Sea by the Italian National Antarctic Program in GBIF.org. Together with other open-access GIS data sources and tools it allows generating, for the first time, three-dimensional predictive distribution maps for twenty-six copepod species. These predictive maps were obtained by applying machine learning techniques to grey literature data, which were visualized in open-source GIS platforms. In a Species Distribution Modeling (SDM) framework we used machine learning with three types of algorithms (TreeNet, RandomForest and Ensemble) to analyze the presence and absence of copepods at different areas and depth classes in function of environmental descriptors obtained from the Polar Macroscope Layers present in Quantartica. The models allow for the first time to map-predict the food chain in quantitative terms showing the relative index of occurrence (RIO) and identified the presence for each copepod species analyzed in the Ross Sea. Our results show marked geographical preferences that vary with species and trophic strategy. This study demonstrates that machine learning is a successful method in accurately predicting Antarctic copepod presence, also providing useful data to orient future sampling and management of wildlife and conservation.</p>
Biodiversity patterns of epipelagic copepods in the South Pacific Ocean: Strengths and limitations of current data bases
<p>These data were used for the development of the paper "<strong>Biodiversity patterns of epipelagic copepods in the South Pacific Ocean: Strengths and limitations of current data bases</strong>". Especifically, we added ecological and environmental data that were used for modeling.</p>
Figure 1 in Molecular evidence on evolutionary switching from particle-feeding to sophisticated carnivory in the calanoid copepod family Heterorhabdidae: drastic and rapid changes in functions of homologues
Figure 1. Morphology-based phylogenetic trees of the heterorhabdids. A and B, Ohtsuka et al. (1997); C, Park (2001).
Figure 6 in Spatiotemporal distribution of planktonic copepod communities in Tokyo Bay where Oithona davisae Ferrari and Orsi dominated in mid-1980s
Figure 6. Horizontal distributions of the identified community groups in Tokyo Bay (the letters in parentheses in legends show the indicator species).
Figure 3 in Seasonal changes in the population structure of dominant planktonic copepods collected using a sediment trap moored in the western Arctic Ocean
Figure 3. Seasonal changes in sea ice concentration, surface chl. a (from satellite) and total mass flux (a), and daylight hours (b) at St. NAPt from October 2010 to September 2012.
Figure 8 in Seasonal changes in the population structure of dominant planktonic copepods collected using a sediment trap moored in the western Arctic Ocean
Figure 8. Seasonal changes in sea ice concentration, daylight hours, chl. a, and total mass flux from January to December (upper panel). The ecological characteristics of the five dominant copepods (lower panel). The open and solid bars indicate the high abundance and reproductive periods for each species, respectively.
Figure 4 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 4. Copepod species composition (centre) and copepodid stage structures of the dominant species (left: Oyashio region, right: Okhotsk Sea). All data are integrated means of a 0– 500 m water column based on the IONESS samples in the Oyashio region (St. 19) and Okhotsk Sea (St. OK24) from October to November 1996. Error bars for the copepodid stage indicate standard deviations of each daily duplicate.
Figure 3 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 3. Vertical distribution of zooplankton biovolume in the Oyashio region (upper panels) and Okhotsk Sea (lower panels) from September to December in 1996–1998. Note that the biovolume axes are not the same between panels. Tc: thermocline.
Illuminating the planktonic stages of salmon lice: a unique fluorescence signal for rapid identification of a rare copepod in zooplankton assemblages.
<p>The Excitation Emission Matrix (EEM) measurements were taken with Shimadzu's proprietary software ‘LabSolutions RF’. All files are in the exported csv format with columns representing the excitation wavelengths and rows the emission wavelengths. Wavelengths range from 200-600 nm with a 2 nm increment. Fluorescence intensity was influenced by the fluctuating number of animals in the path of the excitation beam during the 5 minute measurement. We compensated for this artefact by repeating measurements of each sample five times, calculating the mean, and applying a smoothing function which found the median value within 10 nm. The fluorescence intensity was further normalized on a 0 to 1 scale by dividing intensity by the maximum fluorescence within each EEM measurement.</p> <p>Supplemental Table 1. The metadata of EEM measurements. The measurements were used for the spectrum section analysis and correspond to those depicted in Figures 2, 3, 4, & 5. See sections 3.1, 3.1.1, & 3.1.2. The Sample column indicates which lab culture cohort the sea lice came from (BGO*), which wild caught fish sample they came from (WC*), or the sampling date of non-target copepods (DDMMYY). The filename of each mean measurement is listed and indicates the first of 5 repeated measurements. Corresponding files can be found in the deposited.csv files at Zendo. In those files, data columns represent the excitation wavelengths, 200nm to 600nm increasing in 2 nm increments. Likewise, the rows represent the emission wavelengths. NaN’s are present where scattering layers were removed. All fluorescence intensity values are normalized to the maximum within each EEM.</p>
FIGURE 8 in Four anchimolgid copepods (Poecilostomatoida: Anchimolgidae) associated with the scleractinian coral Pavona explanulata (Lamarck, 1816) in Taiwan
FIGURE 8. Sociellus subgeminus sp. nov. (female). A, habitus, dorsal; B, habitus, lateral; C, urosome; D, caudal ramus; E, antennule; F, antenna G, mandible; H, maxillule; I, maxilla; J, maxilliped. Scale bars: A – B = 0.2 mm; C = 0.1 mm; D – J = 0.02 mm.
FIGURE 5 in Four anchimolgid copepods (Poecilostomatoida: Anchimolgidae) associated with the scleractinian coral Pavona explanulata (Lamarck, 1816) in Taiwan
FIGURE 5. Odontomolgus cognatus sp. nov. (female). A, leg 1; B, leg 2; C, leg 3; D, leg 4; E, leg 5. Scale bars: A – E = 0.05 mm.
FIGURE 2 in Four anchimolgid copepods (Poecilostomatoida: Anchimolgidae) associated with the scleractinian coral Pavona explanulata (Lamarck, 1816) in Taiwan
FIGURE 2. Alienigena triangula gen. et sp. nov. (female). A, leg 2; B, leg 3; C, leg 4; D, leg 5; E, leg 6. Scale bars: A – E = 0.02 mm.
FIGURE 7. Odontomolgus mucosus Kim, 2006 in Four anchimolgid copepods (Poecilostomatoida: Anchimolgidae) associated with the scleractinian coral Pavona explanulata (Lamarck, 1816) in Taiwan
FIGURE 7. Odontomolgus mucosus Kim, 2006 (female: A – G; male: H – I). A, habitus, dorsal; B, antennule; C, mandible; D, maxillule; E, maxilla; F, maxilliped; G, leg 5; H, habitus, dorsal; I, male, maxilliped. Scale bars: A, H = 0.2 mm; B = 0.04 mm; C – F = 0.02 mm; G, I = 0.05 mm.
FIGURE 6 in Four anchimolgid copepods (Poecilostomatoida: Anchimolgidae) associated with the scleractinian coral Pavona explanulata (Lamarck, 1816) in Taiwan
FIGURE 6. Odontomolgus cognatus sp. nov. (male). A, habitus, dorsal; B, antenna; C, maxilliped; D, leg 1. Scale bars: A = 0.2 mm; B – D = 0.05 mm.
FIGURE 1 in Four anchimolgid copepods (Poecilostomatoida: Anchimolgidae) associated with the scleractinian coral Pavona explanulata (Lamarck, 1816) in Taiwan
FIGURE 1. Alienigena triangula gen. et sp. nov. (female). A, habitus, dorsal; B, habitus, lateral; C, urosome; D, caudal ramus; E, antennule; F, antenna; G, mandible; H, maxillule; I, maxilla; J, maxilliped; K, leg 1. Scale bars: A – B = 0.2 mm; C = 0.1 mm; D – K = 0.02 mm.
FIGURES 32 – 39 in Parasitic copepods infesting the olfactory sacs of skates from the southwestern Atlantic with the description of a new species of Kroeyerina Wilson, 1932
FIGURES 32 – 39. Kroeyerina sudamericana sp. nov. SEM micrographs (adult female). 32, general habitus, ventral; 33, caudal rami; 34, detail of distal armature of caudal ramus; 35, fifth leg; 36, rostral processes; 37, mouth tube and maxillules; 38, maxilla; 39, maxilliped. Scale bars: 32 = 500 µm; 33, 37, 39 = 50 µm; 34 – 36 = 10 µm; 38 = 20 µm.
FIGURES 48 – 56. Brianella corniger Wilson, 1915 in Parasitic copepods infesting the olfactory sacs of skates from the southwestern Atlantic with the description of a new species of Kroeyerina Wilson, 1932
FIGURES 48 – 56. Brianella corniger Wilson, 1915. SEM micrographs (female). 48, tip of cephalothorax (oral region), ventral; 49, tip of antennule; 50, antenna (arrows indicate the three naked setae); 51, maxillule; 52, mouth tube, with tips of mandibles inside, 53; fused tip of maxillae and origin of the two processes of the attachment organ (distal portion of maxillae); 54, detail of vestigial bulla; 55, attachment organ; 56, attachment organ (dissected from base) showing asymmetric branching. Scale bars: 48, 54 = 50 µm; 49, 52 = 10 µm; 50 – 51 = 20 µm; 53 = 200 µm; 55 – 56 = 1 mm.
FIGURES 40 – 47 in Parasitic copepods infesting the olfactory sacs of skates from the southwestern Atlantic with the description of a new species of Kroeyerina Wilson, 1932
FIGURES 40 – 47. Kroeyerina sudamericana sp. nov. SEM micrographs (adult male). 40, general habitus, ventral; 41, caudal rami; 42, detail of distal armature of caudal rami; 43, spinulation in lateral fields of genital complex; 44, rostral processes; 45, antenna; 46, mouth tube and maxilla; 47, maxilliped. Scale bars: 40 = 200 µm; 41 = 50 µm; 42 – 44 = 10 µm; 45 – 47 = 20 µm.
FIGURE 3 in Four anchimolgid copepods (Poecilostomatoida: Anchimolgidae) associated with the scleractinian coral Pavona explanulata (Lamarck, 1816) in Taiwan
FIGURE 3. Alienigena triangula gen. et sp. nov. (male). A, habitus, dorsal; B, habitus, lateral; C, maxilliped; D, leg 5; E, leg 6. Scale bars: A – B = 0.2 mm; C – E = 0.02 mm.
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.