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355 results for “data extraction”
Invasion Biology WikiProject Scientific Papers: Text Data Mining and LLM-based Information Extraction of Species, Locations, Habitats, and Ecosystems
<p>This dataset contains the abstract and full-text for publication DOIs from the Invasion Biology WikiProject (DOI: <a href="https://www.doi.org/10.5281/zenodo.12518036">10.5281/zenodo.12518036</a>). The data was retrieved using the <a href="https://ask.orkg.org/">ask.orkg.org</a> <a href="https://api.ask.orkg.org/docs#tag/Semantic-Neural-Search/operation/explore_documents_index_explore_get">API</a>. For the <a href="https://github.com/jd-coderepos/invasion-biology-IE/blob/main/scripts/ask-doi-list-fulltext-search.py">script</a> used to obtain the data, refer to the accompanying GitHub repository: <a href="https://github.com/jd-coderepos/invasion-biology-IE/" target="_blank" rel="noopener">https://github.com/jd-coderepos/invasion-biology-IE/</a>.</p> <p>The resulting CSV file includes the following fields: <code>"ASK ID"</code>, <code>"DOI"</code>, <code>"Title"</code>, <code>"Abstract"</code>, and <code>"Full-text"</code>.</p> <p>Of the 49,438 queried DOIs, the ASK database provided:</p> <ul> <li><strong>Total DOIs processed:</strong> 12,636</li> <li><strong>DOIs with neither abstract nor full-text:</strong> 36 (abstract token count was less than 10)</li> <li><strong>DOIs with abstracts but no full-text:</strong> 12,636</li> <li><strong>DOIs with both abstract and full-text:</strong> 2,834</li> </ul> <p>The second part of the dataset contains structured information extracted from the publications using the GPT-4o Large Language Model. This structured data is included in the zipped folder <code>structured-publications.zip</code>.</p> <p>The accompanying GitHub repository provides access to the code and scripts used at various stages of the information extraction (IE) process.</p> <p><strong>Theme of the Study:</strong><br>"Mining for Species, Locations, Habitats, and Ecosystems from Scientific Papers in Invasion Biology: A Large-Scale Exploratory Study with Large Language Models."</p>
Seasonal sea ice indices including the timing of ice-edge advance and ice-edge retreat (in year day), the ice season duration (in days) and number of actual ice days (versus open water days) within the ice season, extracted for various PAL LTER sub-regions West of the Antarctic Peninsula and derived from passive microwave satellite data for 1979/80 to 2023/24 ice seasons.
Seasonal sea ice indices including the timing of ice-edge advance and ice-edge retreat (in year day), the ice season duration (in days) and number of actual ice days (versus open water days) within the ice season, extracted for various PAL LTER sub-regions West of the Antarctic Peninsula and derived from passive microwave satellite data for 1979/80 to 2023/24 ice seasons. The ice season duration is defined as the time elapsed between day of ice-edge advance and day of ice-edge retreat within a given sea ice year, which begins mid-February (mean minimum of summer sea ice extent for the Southern Ocean) and ends the following mid-February. See Stammerjohn et al (2008, JGR) for further details.
Data for the extraction of the critical temperature of niobium films deposited on copper produced at CERN for SRF applications
<p>Each data set contains the voltage signal amplitude induced in a pickup coil by an alternating magnetic field, crossing the niobium-film-on-copper sample during its state transition from normal conducting to superconducting, the corresponding sample temperature and the estimated errors for the two measured quantities. File columns: #1 sample temperature in Kelvin, #2 estimated temperature error, #3 voltage amplitude in pickup coil in Volt, #4 estimated amplitude error.</p> <p>One data set corresponds to one sample. The critical temperature can be extracted as fit parameter by fitting the amplitude versus temperature data with a logistic function, where it corresponds to the half height of the state transition curve.</p>
TDA4ContextualEmbeddings - Public - Debug Data for the codebase of the publication "Local Topology Measures of Contextual Language Model Latent Spaces With Applications to Dialogue Term Extraction"
<p>Debug dataset for testing the <a href="https://gitlab.cs.uni-duesseldorf.de/general/dsml/tda4contextualembeddings-public">codebase</a> of the paper <a href="https://doi.org/10.18653/v1/2024.sigdial-1.31">“Local Topology Measures of Contextual Language Model Latent Spaces With Applications to Dialogue Term Extraction”</a> published at the 25th Meeting of the Special Interest Group on Discourse and Dialogue, Kyoto, Japan (SIGDIAL 2024).</p>
Data Source: Synergistic effects of precipitation and groundwater extraction on freshwater wetland inundation
Wetlands provide essential ecosystem services, including nutrient cycling, flood protection, and biodiversity support, that are sensitive to changes in wetland hydrology. Wetland hydrological inputs come from precipitation, groundwater discharge, and surface run-off. Changes to these inputs via climate variation, groundwater extraction, and land development may alter the timing and magnitude of wetland inundation. Data were compiled for 152 wetlands in west-central Florida over 14 years to investigate the response of wetland inundation to the interactive effects of precipitation, groundwater extraction, surrounding land development, basin geomorphology, and wetland vegetation class. Further methods are defined in the Methods section of the journal article associated with this dataset (Synergistic effects of precipitation and groundwater extraction on freshwater wetland inundation, published in the Journal of Environmental Management, 2023).
A Data Set of 255,000 Randomly Selected and Manually Classified Extracted Ion Chromatograms for Evaluation of Peak Detection Methods
<p>Non-targeted mass spectrometry (MS) has become an important method over the last years in the fields of metabolomics and environmental research. While more and more algorithms and workflows become available to process a large number of data sets nontargeted, there still exist few manually evaluated universal test data sets for refining and evaluating these methods. The first step of non-targeted screening, peak detection (and refinement of it) is arguably the most important step for non-targeted screening. However, the absence of a model data set makes it harder for researchers to evaluate peak detection methods. In this Data Descriptor, we provide a manually checked data set consisting of 255,000 EICs (5000 peaks randomly sampled from across 51 samples) for the evaluation on peak detection and gap filling algorithms. The data set was created from a previous real-world study, of which a subset was used to extract and manually classify ion chromatograms by three mass spectrometry experts. The data set consists of:</p> <ul> <li>51 converted mass spectral files in mzML format</li> <li>An .RData-file containing the extracted ion chromtograms (EICs)</li> <li>The randomly selected subset and the original output table of MZmine in .csv-format</li> <li>Example .xlsx files for the classification</li> <li>2 central classification tables</li> <li>Several tables with additional information about the sampling, chemical analysis and expert jugdement on EICs</li> </ul> <p>For a full description of the experiment and the data set, please read the related Data Descriptor with the title "A data set of 255000 randomly selected and manually classified extracted ion chromatograms for evaluation of peak detection methods" in Metabolites (https://www.mdpi.com/journal/metabolites; DOI: https://doi.org/10.3390/metabo10040162).</p>
Topography extraction and topographic change measurements using PlanetScope data: Shisper Glacier (Pakistan)
<p>The study area is located in the north flank of Hunza Valley in the Central Karakoram. Shisper glacier covers ~53.7 km2 at an elevation range of 2567-611 m a.s.l. It is a surge-type glacier, which has recently gained the attention of the scientific community and disaster response agencies during its surge. In 2018, the glacier surged beyond the confluence with the outlet stream of Mochwar glacier. The blockage resulted in the creation of a lake, which then drained causing a GLOF (Glacial Lake Outbreak Flood) and has recently begun reforming. The melt water from the two glaciers feeds hydropower plants in the Hunza valley and is a major source of fresh water for agriculture. Glacier-related hazards threaten both the town of Hassanabad and the Karakoram Highway, the only paved road through the mountain range. Here we show the potential of CubSat data to monitor such glaciers, which are not easily accessible to field observation and their potential impact on power generation, water resources and infrastructure.</p> <p>We use multi-date L1B DOVE-C PlanetScope data to extract two DEMs in 2017 and 2019 over the study area in order to compute the elevation difference caused by the glacier surge.</p> <p>Supplementary material for our paper: Optimization of optical image geometric modeling, application to topography extraction and topographic change measurements using PlanetScope and SkySat imagery.</p>
Data Set of Extracted Summary Statistics from Equipment Sensor Data
<p>This data set was generated in accordance with the semiconductor industry and contains values of summary statistics from sensor recordings of the high-precision and high-tech production equipment. Basically, the semiconductor production consists of hundreds of process steps performing physical and chemical operations on so-called wafers, i.e. slices based on semiconductor material. In the production chain, each process equipment is equipped with several sensors recording physical parameters like gas flow, temperature, voltage, etc., resulting in so-called sensor data. Out of the sensor data, values of summary statistics are extracted. These are values like mean, standard deviation and gradients. To keep the entire production as stable as possible, these values are used to monitor the whole production in order to intervene in case of deviations.</p> <p>After the production, each device on the wafer is tested in the most careful way resulting in so-called wafer test data. In some cases, suspicious patterns occur in the wafer test data potentially leading to failure. In this case the root cause must be found in the production chain. For this purpose, the given data is provided. The aim is to find correlations between the wafer test data and the values of summary statistics in order to identify the root cause.</p> <p>The given data is divided into four data sets: "XTrain.csv", "YTrain.csv", "XTest.csv" and "YTest.csv". "XTrain.csv" and "XTest.csv" represent the values of summary statistics originating in the production chain separated for the purpose of training and validating a statistical model. Included are 114 observations of 77 parameters (values of summary statistics). The "YTrain.csv" and "YTest.csv" contain the corresponding wafer test data (144 observations of one parameter).</p>
Deep learning to extract the meteorological by-catch of wildlife cameras: Supporting data, models and code
<p>This repository contains the data, models and code to train and deploy deep learning models related to the paper "Deep learning to extract the meteorological by-catch of wildlife cameras" published in the journal Global Change Biology (<a href="https://doi.org/10.1111/gcb.17078"><strong>https://doi.org/10.1111/gcb.17078</strong></a>).</p>
Extracted raw data from: Global dominance of lianas over trees is driven by forest disturbance, climate, and topography
<p>In a meta-analysis, we use an unprecedented dataset, representing 556 unique locations worldwide, distributed across 44 countries and six continents to show for the first time that lianas (woody vines) thrive relatively better than trees when forests are disturbed, temperature increase, precipitation decrease, and particularly in tropical lowlands. We demonstrate that liana dominance can persist for decades post-disturbance and hinder the recovery of disturbed forests, especially when climate favours lianas. With implications for the global carbon sink, our findings suggest that degraded tropical forests with environmental conditions favouring lianas should be the highest priority to consider for restoration management.</p>
Definitions of terms extracted from data-related European Union laws, version 3
<p>Collection of definitions of terms in English, French, German, Italian and Spanish extracted from the following data-related European laws:</p> <ol> <li> <p><a href="http://data.europa.eu/eli/dir/2007/2/oj?locale=en">Directive 2007/2/EC of the European Parliament and of the Council of 14 March 2007 establishing an Infrastructure for Spatial Information in the European Community (<strong>INSPIRE</strong>)</a></p> </li> <li> <p><a href="http://data.europa.eu/eli/reg/2016/679/2016-05-04?locale=en">Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (<strong>General Data Protection Regulation</strong>) (Text with EEA relevance)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reco/2018/790/oj?locale=en">Commission Recommendation (EU) 2018/790 of 25 April 2018 on <strong>access to and preservation of scientific information</strong></a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg/2018/1807/oj?locale=en">Regulation (EU) 2018/1807 of the European Parliament and of the Council of 14 November 2018 on a framework for the <strong>free flow of non-personal data</strong> in the European Union (Text with EEA relevance)</a></p> </li> <li> <p><a href="https://data.europa.eu/eli/dir/2019/790/oj?locale=en">Directive (EU) 2019/790 of the European Parliament and of the Council of 17 April 2019 on <strong>copyright and related rights in the Digital Single Market</strong> and amending Directives 96/9/EC and 2001/29/EC (Text with EEA relevance)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/dir/2019/1024/oj?locale=en">Directive (EU) 2019/1024 of the European Parliament and of the Council of 20 June 2019 on open data and the re-use of public sector information (recast) (<strong>Open Data Directive</strong>)</a></p> </li> <li><a href="https://eur-lex.europa.eu/eli/reg/2021/695/oj?locale=en">Regulation (EU) 2021/695 of the European Parliament and of the Council of 28 April 2021 establishing <strong>Horizon Europe</strong> – the Framework Programme for Research and Innovation, laying down its rules for participation and dissemination, and repealing Regulations (EU) No 1290/2013 and (EU) No 1291/2013 (Text with EEA relevance)</a></li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg/2022/868/oj?locale=en">Regulation (EU) 2022/868 of the European Parliament and of the Council of 30 May 2022 on European data governance and amending Regulation (EU) 2018/1724 (<strong>Data Governance Act</strong>) (Text with EEA relevance)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg/2022/1925/oj?locale=en">Regulation (EU) 2022/1925 of the European Parliament and of the Council of 14 September 2022 on contestable and fair markets in the digital sector and amending Directives (EU) 2019/1937 and (EU) 2020/1828 (<strong>Digital Markets Act</strong>) (Text with EEA relevance)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg/2022/2065/oj?locale=en">Regulation (EU) 2022/2065 of the European Parliament and of the Council of 19 October 2022 on a Single Market For Digital Services and amending Directive 2000/31/EC (<strong>Digital Services Act</strong>) (Text with EEA relevance)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg_impl/2023/138/oj?locale=en">Commission Implementing Regulation (EU) 2023/138 of 21 December 2022 laying down a list of specific <strong>high-value datasets</strong> and the arrangements for their publication and re-use (Text with EEA relevance)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg/2023/2854/oj?locale=en">Regulation (EU) 2023/2854 of the European Parliament and of the Council of 13 December 2023 on harmonised rules on fair access to and use of data and amending Regulation (EU) 2017/2394 and Directive (EU) 2020/1828 (<strong>Data Act</strong>)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg/2024/903/oj?locale=en">Regulation (EU) 2024/903 of the European Parliament and of the Council of 13 March 2024 laying down measures for a high level of public sector interoperability across the Union (<strong>Interoperable Europe Act</strong>)</a></p> </li> <li> <p><a href="https://eur-lex.europa.eu/eli/reg/2024/1689/oj?locale=en">Regulation (EU) 2024/1689 of the European Parliament and of the Council of 13 June 2024 laying down harmonised rules on artificial intelligence and amending Regulations (EC) No 300/2008, (EU) No 167/2013, (EU) No 168/2013, (EU) 2018/858, (EU) 2018/1139 and (EU) 2019/2144 and Directives 2014/90/EU, (EU) 2016/797 and (EU) 2020/1828 (<strong>Artificial Intelligence Act</strong>) Text with EEA relevance.</a></p> </li> <li><a href="https://eur-lex.europa.eu/eli/reg/2024/2847/oj?locale=en">Regulation (EU) 2024/2847 of the European Parliament and of the Council of 23 October 2024 on horizontal cybersecurity requirements for products with digital elements and amending Regulations (EU) No 168/2013 and (EU) 2019/1020 and Directive (EU) 2020/1828 (<strong>Cyber Resilience Act</strong>) (Text with EEA relevance)</a></li> </ol>
Data for: Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its Daphnia host
<p>This dataset supports the findings of the study 'Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its <em>Daphnia</em> host', published in Hydrobiologia (https://doi.org/10.1007/s10750-022-04889-7)</p>
MMoveT15: A Twitter Dataset for Extracting and Analysing Migration-Movement Data of the European Migration Crisis 2015
<p>In the 2015 migration crisis thousands of refugees and migrants crossed the border to Hungary, Austria and Germany. The movements of these people are reflected in social media, especially on Twitter. We present a dataset of 3275 Tweets form the months September and October 2015. These Tweets are annotated regarding their relevance to the quantitative movement of refugees/migrants into Hungary, Austria and Germany. We present this dataset for a posterior analysis of the 2015 migration crisis or as a basis for an early warning or forecasting system</p>
Additional data for publication: Simple protocol for combined extraction of exocrine secretions and RNA in small arthropods.
<p>Additional data and results are given in this repository. It contains the trimmed reads (fastp; raw reads also on SRA accession numbers SRR29851544-SRR29851549, Bioproject PRJNA1136254), full busco reports for individual transcriptomes, assembly of all six RNAseqs together (transcriptome as base for differential expression analysis) and results of salmon.</p>
Data and Code for "Extracting reproductive parameters from GPS tracking data for a nesting raptor in Europe"
<p>Understanding population dynamics requires estimation of demographic parameters. We build on existing approaches to develop a new tool that uses GPS tracking data to estimate breeding propensity and breeding success, and show that this tool yielded accurate predictions for two red kite populations in Central Europe. The tool is available as an R package at <a href="https://github.com/Vogelwarte/NestTool">https://github.com/Vogelwarte/NestTool</a> and will facilitate the estimation of demographic parameters from tracking data to inform population assessments. The files in this repository contain the data and analytical code to replicate the results of the publication in the Journal of Avian Biology (DOI: 10.1111/jav.03246). The version contained in this repository does not include updates and improvements that occurred after the 29 August 2024.</p>
Formal Methods in Railways: a Systematic Mapping Study - List of Primary Studies and Data Extraction
<p>This Excel file includes the list of papers analyzed in the systematic mapping study titled "Formal Methods in Railways: a Systematic Mapping Study". The study has been submitted for publication, and its preprint is also included in this repository. </p>
Supporting Data -- Evaluating Mask R-CNN Models to Extract Terracing across Oceanic High Islands: an example from Sāmoa.
<p>This dataset provides supplemental information for the manuscript, "Diverse terracing practices revealed by automated lidar analysis across the Sāmoan islands", submitted to Archaeological Prospection. The dataset contains a trained Mask R-CNN deep learning model designed for detecting archaeological terracing features on the islands of American Samoa, associated training data, and the raw and cleaned output of detected terraces.</p>
Numerical convergence of model Cauchy-Characteristic Extraction and Matching (data)
<p>This dataset was used to produce the convergence plots in the paper "Numerical convergence of model Cauchy-Characteristic Extraction and Matching", as well as additional convergence tests that can be found in the repository https://github.com/ThanasisGiannakopoulos/model_CCE_CCM_public. The data can be used to reproduce the aforementioned convergence plots or for comparison against data obtained if one performs the same simulations independently.</p>
Single-cell information extracted from IMC example data
<p>If you are working with these files, please cite them as follows:<br><br>Windhager, J., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc (2023). <a href="https://doi.org/10.1038/s41596-023-00881-0">https://doi.org/10.1038/s41596-023-00881-0</a></p><p>This repository contains additional information related to IMC example data available at <a href="https://zenodo.org/record/5949116">zenodo.org/record/5949116</a>. The following files are available and are part of the <a href="https://bodenmillergroup.github.io/IMCDataAnalysis/">IMC Data Analysis workflow</a></p><ul><li><strong>gated_cells.zip:</strong> contains SpatialExperiment objects storing cells that were manually gated based on their expression values to derive ground truth cell phenotype labels.</li><li><strong>spe.rds:</strong> SpatialExperiment object containing the single-cell information (mean intensity per cell and per channel; cellular metadata; channel metadata) of the processed data.</li><li><strong>images.rds:</strong> CytoImageList object containing the spillover-corrected images.</li><li><strong>masks.rds:</strong> CytoImageList object containing the segmentation masks.</li></ul>
Data Extraction table summarizing studies in the scoping review on co-creation of patient education materials
<p>Data extraction table for scoping review on best practices for co-creating patient-facing educational materials</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.