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.
123
datasets available to search
ShareScore release 0.9.0
Dataset results
123 results for “species database”
FIGURE 8 in Making future taxonomy of Niphargus (Crustacea: Amphipoda: Niphargidae) in the Middle East easier: DELTA database of Middle East species with description of four new species from Iran
FIGURE 8. Niphargus borisi, sp. nov., Belqais Spring, male 9 mm (holotype). A, P 3; B, P 4; C, P 5; D, P 6; E, P 7. Scale bars: 1mm.
FIGURE 4 in Making future taxonomy of Niphargus (Crustacea: Amphipoda: Niphargidae) in the Middle East easier: DELTA database of Middle East species with description of four new species from Iran
FIGURE 4. Niphargus bisitunicus, sp. nov., Sarab-e- Bisitun, male 9 mm (holotype). A, P 3; B, P 4; C, P 5; D, P 6; E, P 7. Scale bars: 1mm.
The Forest Species Database (FSD)
<p>The Forest Species Database (FSD) is composed of 2,240 microscopic images from 112 different species from two groups (Hardwood and Softwood), 85 genera and 30 families, . The images were acquired from the sheets of wood using a Olympus Cx40 microscope with 100 times zoom. The resulting color images were saved in PNG (Portable Network Graphics) format with no compression and a resolution of 1024 × 768 pixels. The figure below provides some samples of the database.</p><p>The FSD 1.0 is structured as follows:</p><ul><li>112 species – 20 images per species = 2,240 images.</li></ul><p>The FS Database may be used for non-commercial research provided you acknowledge the source of the image by citing the following paper in publications about your research:</p><ul><li>J. Martins, L. S. Oliveira, S. Nigkoski, R. Sabourin, <strong>A Database for Automatic Classification of Forest Species</strong>, Machine Vision and Applications, 24(3): 567-578, 2013. (<a href="http://www.inf.ufpr.br/lesoliveira/download/MVA2012.pdf">pdf</a>)</li></ul>
Forest Species Database – Macroscopic (FSD-M)
<p>The Forest Species Database – Macroscopic (FSD-M) is composed of 2,942 macroscopic images from 41 different forest species of the Brazilian flora. The database was collected using a Sony DSC T20 with the macro function activated. The resulting images are then saved in JPG format with no compression and a resolution of 3264 × 2448 pixels.The figure below provides some samples of the database.</p><p>The FSD-M Database may be used for non-commercial research provided you acknowledge the source of the image by citing the following paper in publications about your research:</p><ul><li>P. L. Paula Filho, L. S. Oliveira, S. Nigkoski, A. S. Britto Jr, <a href="http://www.inf.ufpr.br/lesoliveira/download/MVA2014.pdf"><strong>Forest Species Recognition using Macroscopic Images</strong></a>, Machine Vision and Applications<strong>, </strong>25(4):1019-1031, 2014.</li></ul><p>Please note that the number of images for each class has been increased since the publication of the first version of this dataset. </p>
Observations of Jordanita species in Central Europe from the BioOffice database, Tyolean state museum
<p><span>The decline of biodiversity in general and of insect diversity in particular has been recognized as a major environmental problem in recent years. </span><span>The study of Markl et al., in which this dataset was used, reports the distribution and the decline of populations of forester moths of the genus Jordanita in Central Europe since 1950 as a type example of the loss of grassland biodiversity, and discusses the reasons for this decline. </span><span>Based on extensive work in museums and private collections, a literature review and own observations, and including data as far back as 1834, this genus helps to understand the deeper reasons of insect population and biodiversity decline, as the well investigated six Central European species cover a broad range of extensive grassland habitats (fens to low-production grassland and xerothermic steppes) from low altitudes to high alpine meadows. Therefore, they monitor processes relevant also to other, less investigated grassland species. </span></p>
Supplementary material 2 from: Grimm A, Ramírez AMP, Moulherat S, Reynaud J, Henle K (2014) Life-history trait database of European reptile species. Nature Conservation 9: 45-67. https://doi.org/10.3897/natureconservation.9.8908
Comments on taxonomy and species coverage: Explanation note: The supplementary material consists of several tables that explain differences between our updated list of species names to the lists used by Sillero et al. (2014) in their new SEH list of species and the list of Speybroeck et al. (2010).
Supplementary material 1 from: Grimm A, Ramírez AMP, Moulherat S, Reynaud J, Henle K (2014) Life-history trait database of European reptile species. Nature Conservation 9: 45-67. https://doi.org/10.3897/natureconservation.9.8908
Species names used in our database and used in the Societas Europaea Herpetologica (SEH) atlas: Explanation note: The table matches the species names in the SEH atlas with the updated speceis names used in our database. It thus provides the two species list that can be used to search the database.
A database of Defra statutory biodiversity metric unit values for terrestrial habitat samples across England, with plant, butterfly and bird species data
<p>Policies requiring biodiversity no net loss or net gain as an outcome of environmental planning have become more prominent worldwide, catalysing interest in biodiversity offsetting as a mechanism to compensate for development impacts on nature. Offsets rely on credible and evidence-based methods to quantify biodiversity losses and gains. Following the introduction<span> of the United Kingdom's Environment Act in November 2021, all new developments requiring planning permission in England are expected to demonstrate a 10% biodiversity net gain from 2024, calculated using the statutory biodiversity metric framework (Defra, 2023). </span><span>The metric is used to calculate both baseline and proposed post-development biodiversity units, and is </span>set to play an increasingly prominent role in nature conservation nationwide.<span> </span><span>The metric has so far </span>received limited scientific scrutiny.</p> <p><span>This dataset comprises a database of statutory biodiversity metric unit values for terrestrial habitat samples across England. For each habitat sample, we present </span><span>biodiversity units alongside five long-established single-attribute proxies for biodiversity (</span><span>species richness, individual abundance, number of threatened species, mean species range or population, mean species range or population change)</span><span>. </span><span>Data were compiled </span><span>for species from three taxa (vascular plants, butterflies, birds), from sites across England. The dataset includes 24 sites within </span>grassland, wetland, woodland and forest, sparsely vegetated land, cropland, heathland and shrub, i.e. <span>all terrestrial broad habitats except urban and individual trees. Species data were reused from long-term ecological change monitoring datasets</span> (mostly in the public domain), whilst biodiversity units were calculated following field visits. Fieldwork was carried out in April-October 2022 to calculate biodiversity units for the samples. <span>Sites were initially assessed using metric version 3.1, which was current at the time of survey, and were subsequently updated to the statutory metric for analysis using field notes and species data. </span>Species data <span>were derived from </span>24 <span>long-term ecological change monitoring</span> sites across the Environmental Change Network (ECN), Long Term Monitoring Network (LTMN) and Ecological Continuity Trust (ECT), collected between 2010 and 2020.</p>
Body length trait values from the BETSI database, on all Collembola species, all literature sources, requested on 01-06-2017
<p><strong>This table gathers 'Body length' trait values extracted from the BETSI database, on all Collembola species, all literature sources, on 01/06/2017 (DD/MM/YYYY).</strong><br> <br> The BETSI database hosts soil invertebrates trait data.<br> The BETSI database is available here: <a href="http://betsi.cesab.org">http://betsi.cesab.org</a><br> The BETSI database is regularly updated. Please follow the link and contact its administrators if you want to obtain the most up-to-date data ; or contact the dataset's author if you need information on how to use the present dataset.</p> <p><br> <strong>Information in this table</strong><br> <em>BETSI coder</em>: First name and family name of the person that provided the trait value and uploaded it into the BETSI database<br> <em>Collembola species</em>: Collembola species name, taxonomy according to Fauna Europaea<br> <em>Body length value</em>: Trait value, in mm<br> <em>Literature source</em>: Literature source in which the trait value was collected by the BETSI coder<br> <br> This dataset was created, used, and shared with the approval of all concerned BETSI coders (data collectors) and administrators (data managers).</p> <p> </p> <p><strong>If you aim to re-use this dataset:</strong><br> <br> - please cite <strong>Bonfanti et al. (2018) <em>Functional ecology </em></strong><a href="https://doi.org/10.1111/1365-2435.13194">https://doi.org/10.1111/1365-2435.13194</a>, study for which this dataset was originally requested and compiled ;<br> - please give appropriate credit to the concerned BETSI coders and administrators, BETSI database project, and to the authors of the literature sources mentioned in the dataset.</p>
Database of conference proceedings references corresponding to Eimeria species that infect ruminants
<p>Database of conference proceedings references corresponding to Eimeria species that infect ruminants</p>
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7). in An integrative taxonomic revision of the genus Triphosa Stephens, 1829 (Geometridae: Larentiinae) in the Middle East and Central Asia, with description of two new species
APPENDIX. List of sequenced specimens of Triphosa, with identification, Sampling sites collecting data, Accession numbers, and process ID in BOLD database. Data taken from BOLD and generated by Axel Hausmann (1); Bernd Müller (2); Dirk Stadie (3); Iva Mihoci 4); Marco Infusino, Stefano Scalercio (5); Norbert Poell (6); Wanke et al. (7).
FIG. 3 in Thermal Traits of Anurans Database for the Southeastern United States (TRAD): A Database of Thermal Trait Values for 40 Anuran Species
FIG. 3. Adult trait completeness, or number of traits with at least one trait value in the literature, varies among and within anuran genera (A) and families (B). Each y-axis is ordered by the group with the highest trait completion to group with the lowest trait completion. Points represent individual species. Boxplots indicate standard delineations of median, 25th, and 75th percentiles, and lines indicate the lesser of largest or smallest values or 1.5 times the interquartile range.
FIG. 2 in Thermal Traits of Anurans Database for the Southeastern United States (TRAD): A Database of Thermal Trait Values for 40 Anuran Species
FIG. 2. Species' thermal trait data, measured as sources with unique species and trait combinations (points), have increased since 1945.
FIG. 1 in Thermal Traits of Anurans Database for the Southeastern United States (TRAD): A Database of Thermal Trait Values for 40 Anuran Species
FIG. 1. Counts of adult thermal trait values found within the literature for 37 species of frogs and toads (anurans) within the southeastern United States. Species Pseudacris brimleyi, Pseudacris nigrita, and Pseudacris ocularis are not shown due to no trait values reported. States indicated in gray in the inset map of the conterminous United States are considered the southeastern United States for this database. Trait Name is ordered based on type of trait: warm colored traits are mass and physiological traits, and cool colored traits are behavioral traits. Physiological traits include critical thermal maximum (CTmax), critical thermal minimum (CTmin), and Tpref (preferred temperature). Behavioral traits include basking temperature (Tbask), foraging temperature limits (Tforage_min and Tforage_max), emergence temperature (Tmerge), and activity. An * indicates a species of conservation concern. Conservation status, as defined by the International Union for the Conservation of Nature Red List, was determined on 15 August 2020 (International Union for Conservation of Nature, 2017).
FIG. 4 in Thermal Traits of Anurans Database for the Southeastern United States (TRAD): A Database of Thermal Trait Values for 40 Anuran Species
FIG. 4. The number of traits with at least one trait value in the literature (trait completeness) increases with range size for adults (A) and for all life stages (B) for 37 anurans native to the southeastern United States. Maximum trait completeness is 9 for adults and 22 for all life stages. Each point represents a species that has at least one trait value in the TRAD database, with the symbol and shade in (B) representing the total number of life stages (egg/embryo, tadpole, metamorph, juvenile, and adults) with trait data.
Global Invasive Species Database (GISD)
<p>The Global Invasive Species Database is a free, online searchable source of information about alien and invasive species that negatively impact biodiversity. The GISD aims to increase public awareness about invasive species and to facilitate effective prevention and management activities by disseminating specialist__s knowledge and experience to a broad global audience. It focuses on invasive alien species that threaten native biodiversity and natural areas and covers all taxonomic groups from micro-organisms to animals and plants.The Global Invasive Species Database (GISD) is managed by the Invasive Species Specialist Group (ISSG) of the IUCN Species Survival Commission. It was developed between 1998 and 2000 as part of the global initiative on invasive species led by the erstwhile Global Invasive Species Programme (GISP).</p> <p>http://www.iucngisd.org/gisd/about.php</p>
Proteome database of 36 million proteins from 4,351 species, including marine microbial sequences
<p>A fasta-formatted database of 36,866,870 predicted proteins representing 4,351 unique species from 117 phyla.</p>
Homotypic motifs from 5 databases in the promoters of 21 plant species
<p><strong>What is this about:</strong></p> <p>This project encompasses multiple plant species, primarily employing tools like FIMO and PMET index to search for homotypic motifs in the promoters across various plant species. We selected five different sources of motifs: <strong>CIS-BP2</strong>, <strong>Franco-Zorrilla et al. 2014</strong>, <strong>Jaspar plants non redundant 2022</strong>, <strong>PlantTFDB</strong> and <strong>Plant Cistrome DB</strong>.</p> <p>Our research delves into an extensive analysis of gene expression regulatory elements, aiming to unravel the mechanisms of plant gene expression regulation. For this purpose, we have pre-calculated a vast amount of data in order to identify promoter patterns that consistently appear across different species. These promoter patterns potentially play fundamental and crucial regulatory roles in each species.</p> <p><strong>How to use it:</strong></p> <p>All data are prepared for PMET-Shiny app: <a href="https://github.com/duocang/PMET-Shiny-App">https://github.com/duocang/PMET-Shiny-App</a>.</p> <p>After downloading, all files are unzipped and put in the folder of <em><strong>data/indexing</strong></em> of PMET-Shiny.</p>
Observations of Jordanita species in Central Europe from the BioOffice database, Tyolean state museum
Open the record for dataset details and reuse information.
Proteome database of 36 million proteins from 4,351 species, including marine microbial sequences
Open the record for dataset details and reuse information.
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.