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16 results for “Metadata analysis”
MALDI MS data and metadata from "A biocodicological analysis of the medieval library and archive from Orval Abbey, Belgium"
<p>See <a href="https://doi.org/10.1098/rsos.210210">Ruffini-Ronzani et al</a>.</p>
Worldwide Soundscapes project metadata and analysis scripts
<p>The Worldwide Soundscapes project is a global, open inventory of spatio-temporally replicated passive acoustic monitoring meta-datasets (i.e. meta-data collections). This Zenodo entry comprises the data tables that constitute its (meta-)database, as well as their description. Additionally, R scripts are provided to replicate the analysis published in [placeholder].</p> <p>The overview of all sampling sites and timelines can be found on the corresponding project on <a href="https://ecosound-web.de/ecosound_web/collection/index/106">ecoSound-web</a>, as well as a <a href="https://ecosound-web.de/ecosound_web/collection/show/49">demonstration collection</a> containing selected recordings. The recordings of this collection were annotated and analysed to explore macro-ecological trends.</p> <p>The audio recording criteria justifying inclusion into the meta-database are:</p> <ul> <li>Stationary (no transects, towed sensors or microphones mounted on cars)</li> <li>Passive (unattended, no human disturbance by the recordist)</li> <li>Ambient (no directional microphone or triggered recordings, non-experimental conditions)</li> <li>Spatially and/or temporally replicated (i.e. multiple sites sampled at the same time and/or multiple days - covering the same daytime - sampled at the same site)</li> </ul> <p>The individual columns of the provided data tables are described in the following. Data tables are linked through primary keys; joining them will result in a database. The data shared here only includes validated collections.</p> <p><strong>Changes from version 4.0.0</strong></p> <p>Added link to the published synthesis.</p> <p><strong>Meta-database CSV files</strong></p> <p><strong>collections</strong></p> <ul> <li>collection_id: unique integer, primary key</li> <li>name: name of the dataset. if it is repeated, incremental integers should be used in the "subset" column to differentiate them.</li> <li>ecoSound-web_link: link of validated meta-collection on ecoSound-web</li> <li>primary_contributors: full names of people deemed corresponding contributors who are responsible for the dataset</li> <li>secondary_contributors: full names of people who are not primary contributors but who have significantly contributed to the dataset, and who could be contacted for in-depth analyses</li> <li>date_added: when the datased was added (YYYY-MM-DD)</li> <li>URL_open_recordings: internet link for openly-available recordings from this collection</li> <li>URL_project: internet link for further information about the corresponding project</li> <li>DOI_publication: Digital Object Identifiers of corresponding publications</li> <li>core_realm_IUCN: The main, core realm of the dataset according to IUCN Global Ecosystem Typology (v2.0): https://global-ecosystems.org/</li> <li>medium: the physical medium the microphone is situated in</li> <li>locality: optional free text about the locality</li> <li>contributor_comments: free-text field for comments by the primary contributors</li> </ul> <p><strong>collections-sites</strong></p> <ul> <li>dataset_ID: primary key of collections table</li> <li>site_ID: primary key of sites table</li> </ul> <p><strong>sites</strong></p> <ul> <li>site_ID: unique integer, primary key</li> <li>site_name: internal name or code of sampling site as used in respective projects</li> <li>latitude_numeric: site's numeric degrees of latitude</li> <li>longitude_numeric: site's numeric degrees of longitude</li> <li>blurred_coordinates: whether latitude and longitude coordinates are inaccurate, boolean. Coordinates may be blurred with random offsets, rounding, snapping, etc. Indicate the blurring method inside the comments field</li> <li>topography_m: vertical position of the microphone relative to the sea level. for sites on land: elevation. For marine sites: depth (negative). in meters. Only indicate if the values were measured by the collaborator.</li> <li>freshwater_depth_m: microphone depth, only used for sites inside freshwater bodies that also have an elevation value above the sea level</li> <li>realm: Ecosystem type: main realm according to IUCN GET https://global-ecosystems.org/</li> <li>biome: Ecosystem type: main biome according to IUCN GET https://global-ecosystems.org/</li> <li>functional_group: Ecosystem type: main functional group according to IUCN GET https://global-ecosystems.org/</li> <li>contributor_comments: free text field for contributor comments</li> <li>GADM_0: Global ADMinistrative Database level 0 classification of terrestrial site or marine site that is within territorial waters. Source: https://gadm.org/download_world.html</li> <li>IHO: International Hydrographic Organization classification of marine site. Source: https://marineregions.org/downloads.php</li> <li>WDPA: World Database on Protected Areas classification of the site. Source: https://www.protectedplanet.net/en/thematic-areas/wdpa?tab=WDPA</li> </ul> <p><strong>deployments</strong></p> <ul> <li>dataset_ID: primary key of datasets table</li> <li>deployment: identical subscript letters to denote rows that belong to the same deployment. For instance, you may use different operation times and schedules for different target taxa within one deployment.</li> <li>subset_site_ID: If the deployment was not done in all the sites of the corresponding collection, site IDs where the deployment was conducted</li> <li>start_date: date of deployment start</li> <li>start_time_mixed: deployment start local time, either in HH:MM format or a choice of solar daytimes (sunrise, sunset). Corresponds to the recording start time for continuous recording deployments. If multiple start times were used, you should mention the latest start time (corresponds to the earliest daytime from which all recorders are active). If applicable, positive or negative offsets from solar times can be mentioned (For example: if data are collected one hour before sunrise, this will be "sunrise-60")</li> <li>permanent: whether the deployment is permanent, boolean</li> <li>end_date: date of deployment end (date when last scheduled operation starts)</li> <li>end_time_mixed: deployment end local time, either in HH:MM format or a choice of solar daytimes (sunrise, sunset, noon, midnight). Corresponds to the recording end time for continuous recording deployments.</li> <li>operation_mode: continuous: recording takes place from the deployment start date-time to deployment end date-time.<br>periodical: recording takes place periodically (i.e., with duty cycle) from the deployment start date-time to deployment end date-time.<br>scheduled: recording takes place during scheduled daily time intervals (optionally with duty cycle)</li> <li>duty_cycle_minutes: duty cycle of the recording (i.e. the fraction of minutes when it is recording), written as "recording(minutes)/period(minutes)". empty if no duty cycle is used. For example: "1/6" if the recorder is active for 1 minute and standing by for 5 minutes</li> <li>operation_start_time_mixed: only for scheduled recordings: start local time, either in HH:MM format or a choice of solar daytimes (sunrise, sunset, noon, midnight). If applicable, positive or negative offsets from solar times can be mentioned (For example: if data are collected one hour before sunrise, this will be "sunrise-60")</li> <li>operation_duration_minutes: only for scheduled recordings: duration of operation in minutes, if constant</li> <li>operation_end_time_mixed: only for scheduled recordings: end local time, either in HH:MM format or a choice of solar daytimes (sunrise, sunset, noon, midnight). Only required if durations are variable. Do not use when end times are ambiguous (for instance, if a recording could be 1 hour or 25 hours long because the end is on the next day). If applicable, positive or negative offsets from solar times can be mentioned (For example: if data are collected one hour before sunrise, this will be "sunrise-60")</li> <li>high_pass_filter_Hz: frequency of the high-pass filter of the recorder if applied, in Hz. Otherwise, write "none". This may be called a "low-cut" filter too.</li> <li>bit_depth: sampling bit depth of the recordings. Often constant for a particular recorder</li> <li>channels: number of recorded audio channels</li> <li>sampling_frequency_kHz: frequency at which the microphone signal was sampled by the recorder (sounds of half that frequency will be recorded)</li> <li>recorder: recorder used for deployment</li> <li>microphone: microphone used for deployment</li> <li>target_taxa: main IUCN animal taxa that were studied with this deployment, using the exact IUCN Red list names (http://www.iucnredlist.org/), separated by commas. Only genera, families, orders, and classes are accepted. Empty if there was no taxonomic focus (i.e., general soundscapes were the study focus).</li> <li>contributor_comments: free text field for contributor comments</li> <li>exact_recordings: whether the deployment data here have been superseded by inserting more exact recording date-time ranges into the meta-collection on ecoSound-web</li> </ul> <p><strong>recordings (partial download from <a href="https://ecosound-web.de/">ecoSound-web</a>)</strong></p> <ul> <li>recording_id: primary key of the recordings table</li> <li>collection_id: ID of the collection the recording belongs to</li> <li>name: name of the recording</li> <li>site_id: site ID the recording belongs to:</li> <li>recorder_id: ID of the recorder used for the recording (internal ecoSound-web code)</li> <li>microphone_id: ID of the microphone used for the recording (internal ecoSound-web code)</li> <li>recording_gain:recording gain applied for amplifying the audio signal, in decibels</li> <li>duty_cycle_recording: fraction of the recording periode when the recorder is actively recording audio</li> <li>duty_cycle_period: period of the duty cycle, i.e., time between the starts of two subsequent recordings</li> <li>note: comments (contains the target taxon)</li> <li>file_date: date of the recording start</li> <li>file_time: local time of the recording start</li> <li>sampling_rate: audio sampling rate in Hz</li> <li>bitdepth: depth in bits for each audio sample</li> <li>channel_num: number of channels</li> <li>duration: duration of the recording in seconds. Note: duty-cycled recordings cover only a proportion of this duration<strong><br></strong></li> </ul> <p><strong>affiliations</strong></p> <ul> <li>affiliation_id: primary key of affiliations table</li> <li>lab_research_group: Laboratory or research group name</li> <li>department_school_institute: department, school, or institute name</li> <li>university_institution: University or institution name</li> <li>street_address: street address</li> <li>region_state_province_city: region, state, province, or city name</li> <li>postal_code: postal code</li> <li>country: country name</li> </ul> <p><strong>primary_contributors</strong></p> <ul> <li>First_name: First, given name, anonymised when contributor is technically accepted but has not yet given publication authorisation</li> <li>Last_name: Last, family name, anonymised when contributor is technically accepted but has not yet given publication authorisation</li> <li>ORCiD</li> <li>affiliation_IDs: primary keys of the affiliations' table corresponding affiliations, separated by comma</li> <li>first_tier_position: Author position in first-tier</li> <li>publication_agreement: Has contributor explicitly agreed to share her/his meta-data in the collaboration agreement?</li> <li>co_author_first_synthesis: Has contributor confirmed co-authorship intention in the collaboration agreement?</li> </ul> <p>The following columns describe the contributor's role in the project accordint to <a href="https://credit.niso.org/">CRediT</a> taxonomy.</p> <p><strong>Auxiliary files for reproducing analysis</strong></p> <p><strong>R scripts</strong></p> <ul> <li><strong>acoustic analysis.R: </strong>reproduces the result of the soundscape case studies</li> <li><strong>metadata analysis.R:</strong> reproduces the metadata analysis results in the publication</li> </ul> <p><strong>Data from the demonstration collection (download from ecoSound-web)</strong></p> <ul> <li><strong>demo_recordings.csv:</strong> metadata of the recordings, see recordings table</li> <li><strong>demo_sites.csv: </strong>metadata of the sampling locations, see sites table</li> <li><strong>demo_tags.csv: </strong>data describing annotations made in demonstration recordings for the biophony, anthropophony, geophony, and unknown sound sources</li> <li><strong>spectrograms.zip:</strong> contains PNG format spectrograms used in generating Figure 5</li> </ul> <p><strong>Externally sourced data</strong></p> <ul> <li><strong>GET_areas_2.1.1.csv: </strong>raw data obtained from Keith et al. 2023 (https://doi.org/10.5281/zenodo.10081251), then summarized in QGIS to obtain areas per functional group</li> <li><strong>Havlik_sites.csv:</strong> data obtained from Havlik et al. 2022 supplementary material (https://www.frontiersin.org/articles/10.3389/fmars.2022.919418), originally named "Data Sheet 1.CSV"</li> <li><strong>Sugai_sites_updated.csv:</strong> data obtained from Sugai et al. 2019 (https://doi.org/10.1093/biosci/biy147), personal communication with permission</li> <li><strong>taxonomy.csv:</strong> raw data obtained from IUCN Red List for all animal taxa (https://www.iucnredlist.org/)</li> <li><strong>topography_range_latitude.csv:</strong> raw topography from GEBCO sub-ice data (https://www.gebco.net/data_and_products/gridded_bathymetry_data/), summarised by bins of 10 latitudinal rows</li> </ul>
SciKGTeX Scientific Contribution Metadata LaTeX Package User Evaluation Results & Analysis
<p>The responses and measured variables from 26 participants of the first user test of the SciKGTeX package.</p> <p><a href="https://github.com/Christof93/SciKGTeX">https://github.com/Christof93/SciKGTeX</a></p> <p>Also the raw text source for the evaluation tasks and the result analysis notebook with the results saved as tsv file.</p>
Raw and aggregated data for the study introduced in the article "An analysis of citing and referencing habits across all scholarly disciplines: approaches and trends in bibliographic metadata errors"
<p>This dataset contains all the raw data and aggregated data subject of the study introduced in the article "An analysis of citing and referencing habits across all scholarly disciplines: approaches and trends in bibliographic metadata errors". The study is based on the bibliographic and citation data contained in 729 articles published in 147 journals in 27 subject areas. The articles contained a total amount of 34,140 bibliographic references and 55,100 mentions and quotations overall.</p> <p>The dataset is composed of a series of files:</p> <ul> <li>the files "subject_area_<discipline-name>.csv" contain the raw data of the articles published in the journals of all the disciplines considered in the study;</li> <li>the file "article_data_summary.csv" contains the aggregated data created considering the raw data in the previous files, which have been used to creating all the tables and figures in the article;</li> <li>the file "starred_metadata_set.csv" contains information about the most used subset of bibliographic metadata;</li> <li>the file "journals_selection.csv" contains information about all the journals selected for the study.</li> </ul>
Sampling metadata for the publication: "Deep-sea sponge derived environmental DNA analysis reveals demersal fish biodiversity of a remote Arctic ecosystem "
<p>Meta data of sampling location, time and depth of eDNA samples used in the study: "Deep-sea sponge derived environmental DNA analysis reveals demersal fish biodiversity of a remote Arctic ecosystem". As well as taxonomic identification of sponges, their microbial abundance and growth form.</p>
Systematic review and meta-analysis: water type and temperature affect environmental DNA decay metadata
<p>Environmental DNA (eDNA) has been used in a variety of ecological studies and management applications. The rate at which eDNA decays has been widely studied but at present it is difficult to disentangle study-specific effects from factors that universally affect eDNA degradation. To address this, a systematic review and meta-analysis was conducted on aquatic eDNA studies. Analysis revealed eDNA decayed faster at higher temperatures and in marine environments (as opposed to freshwater). DNA type (mitochondrial or nuclear) and fragment length did not affect eDNA decay rate, although a preference for < 200 bp sequences in the available literature means this relationship was not assessed with longer sequences (<em>e.g.</em> > 800 bp). At present, factors such as ultraviolet light, pH, and microbial load lacked sufficient studies to feature in the meta-analysis. Moving forward, we advocate researching these factors to further refine our understanding of eDNA decay in aquatic environments. This dryad entry contains the metadata which formed the basis for the meta-analysis.</p>
Metadata of the Top 40 Journals in Distance Education: A Bibliometric Analysis of Impact 2018-2022
<p>This file contains metadata from the 40 most impactful journals in the field of distance education, selected through a rigorous bibliometric analysis using the SCImago Journal Rank (SJR) indicator provided by SCImago. Two main criteria guided the selection: the first targeted journals ranked in Q1 and Q2 in the specific category of "e-learning" within the social sciences and education area, highlighting publications that demonstrate high impact and relevance in the academic community according to the selected indicator. The second criterion was based on keyword searches in the journal titles, selecting those that include terms like e-learning, online, Distance Education, Technology Learning, Communications in Information, and Information Education and their variants (e.g., plural), also positioned in Q1 or Q2.</p> <p>The metadata, extracted from the Scopus database, covers publications from the period 2018 to 2022 and includes vital information such as document type, authors' names, article title, journal name, publication year, pages, volume, and issue number. Additionally, each article is identified by a Digital Object Identifier (DOI) and URLs for direct access to the full text online, along with abstracts and keywords. These elements together provide a comprehensive and accessible view of the articles, facilitating bibliometric analyses and related academic research.</p> <p>This compilation serves as an essential resource for researchers and educators interested in understanding the dynamics and development of the field of distance education, offering a solid foundation for future investigations and the formulation of evidence-based educational policies.</p>
Systematic review and meta-analysis: water type and temperature affect environmental DNA decay metadata
Open the record for dataset details and reuse information.
Raw reads and metadata for 16S and 12S sequencing for microbiome and dietary analysis of Tasmanian devils
Open the record for dataset details and reuse information.
Metadata of sampling strategy during metabarcoding analysis (Journal publication supplement)
<p>The table presents supplementary materials and contains metadata of sampling strategy during metabarcoding analysis of four types of substrates in two ombrotrophic bog habitats, with other experimental and environmental parameters included in analyses. </p>
Metadata description regarding a study "Competitiveness and value creation: Longitudinal analysis of sawmills and wood construction element producers in Finland"
<p>This dataset is supplied by a commercial information service and is subject to usage restrictions. As such, the dataset itself cannot be publicly shared. This metadata description offers detailed information about the dataset's content and structure.</p>
Figure 4 from: Zaragoza-Tapia F, Pulido-Flores G, Gardner SL, Monks S (2020) Host relationships and geographic distribution of species of Acanthobothrium Blanchard, 1848 (Onchoproteocephalidea, Onchobothriidae) in elasmobranchs: a metadata analysis. ZooKeys 940: 1-49. https://doi.org/10.3897/zookeys.940.46352
Figure 4 Number of species of Acanthobothrium reported from elasmobranchs in each biogeographic region (Last et al. 2016b).
Figure 1 from: Zaragoza-Tapia F, Pulido-Flores G, Gardner SL, Monks S (2020) Host relationships and geographic distribution of species of Acanthobothrium Blanchard, 1848 (Onchoproteocephalidea, Onchobothriidae) in elasmobranchs: a metadata analysis. ZooKeys 940: 1-49. https://doi.org/10.3897/zookeys.940.46352
Figure 1 Type localities of species of Acanthobothrium reported worldwide and the biogeographic regions (Last et al. 2016b) of the geographic distribution of their hosts (see Table 1).
Figure 3 from: Zaragoza-Tapia F, Pulido-Flores G, Gardner SL, Monks S (2020) Host relationships and geographic distribution of species of Acanthobothrium Blanchard, 1848 (Onchoproteocephalidea, Onchobothriidae) in elasmobranchs: a metadata analysis. ZooKeys 940: 1-49. https://doi.org/10.3897/zookeys.940.46352
Figure 3 Families of rays: A number of species of rays per family B number of species of rays parasitized by species of Acanthobothrium. Note: The first number within parentheses corresponds to the number of species of ray that have been reported as hosts of Acanthobothrium and the second is the number of species that have been described from that Family C percentage of species of rays reported to be parasitized within the total number of families of rays- note: Red color = parasitized; Blue color = not parasitized.
Figure 2 from: Zaragoza-Tapia F, Pulido-Flores G, Gardner SL, Monks S (2020) Host relationships and geographic distribution of species of Acanthobothrium Blanchard, 1848 (Onchoproteocephalidea, Onchobothriidae) in elasmobranchs: a metadata analysis. ZooKeys 940: 1-49. https://doi.org/10.3897/zookeys.940.46352
Figure 2 Families of sharks: A number of species of sharks per family B number of species of sharks parasitized by species of Acanthobothrium. Note: The first number within parentheses corresponds to the number of species of shark that have been reported as hosts of Acanthobothrium and the second is the number of species that have been described from that Family C percentage of species of shark reported to be parasitized within the total number of families of sharks- note: Red color = parasitized; Blue color = not parasitized.
Filtered seurat object with metadata and analysis for Figure 4-5
<p>Please see metadata clustering resolution of 0.4 for clusters in figure, and annotations in "NK2". Please use ADT_denoised_iso_quant for adt (protein) normalized data.</p>
ScienceDex guides
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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.