Find research datasets worth reusing

opencc-zeroMar 2023View details →

Open-population SCR model to estimate spatiotemporal variation in individual birth locations, detection rates, and survival

This is an open population SCR model developed by R. Chandler and K. Engebretsen. The full model incorporates 4 spatial covariates in birth location density submodel, 3 location-specific, temporal covariates in the detection submodel, and 4 spatial covariates in the survival submodel. Formatted data is provided for the 2015 and 2016 fawning season in south Florida and the model can be fit using the script fitFawnModel.R.

opencc-by-4.0Apr 2022View details →

Open ENTRANCE Deliverable D3.2 - Supplementary Material

This repository contains the supplementary material for Open ENTRANCE Deliverable D3.2 (https://openentrance.eu/2022/07/06/quantitative-scenarios-for-low-carbon-futures-of-the-european-energy-system-oncountry-region-and-local-level/) It contains all input and output files, including GAMS model files of the used GENeSYS-MOD version (model version v3.1-oE).

opencc-by-4.0Mar 2023View details →

Supporting material for PyESDv1.0.1 An open-source Python framework for empirical-statistical downscaling of climate information

The nature and severity of climate change impacts varies significantly from region to region. Consequently, high-resolution climate information is needed for meaningful impact assessments and the design of mitigation strategies. This demand has led to an increase in the coupling of Empirical Statistical Downscaling (ESD) models to General Circulation Model (GCM) simulations of future climate. Here, we present a new open-source Python package (pyESD; github.com/Dan-Boat/PyESD) that implements several Perfect Prognosis ESD (PP-ESD) methods and the whole downscaling cycle. The latter includes routines for data preparation, predictor selection and construction, model selection and training, evaluation, utility tools for relevant statistical tests, visualization, and more. The package includes a collection of well-established Machine Learning algorithms and allows the user to choose a variety of estimators, cross-validation schemes, objective function measures, hyperparameter optimization, etc., in relatively few lines of code. The package is highly modular and flexible and allows quick and reproducible downscaling of any climate information, such as precipitation, temperature, wind speed, or even glacial retreat. The dataset presented here serves as supporting material for the package description and evaluation manuscript

opencc-by-sa-4.0Mar 2023View details →

unarXive: All arXiv Publications Pre-Processed for NLP, Including Structured Full-Text and Citation Network (open subset)

<h2>Description</h2>unarXive is a scholarly data set containing publications' structured full-text, annotated in-text citations, linked non-text content (mathematical notation, figure/table captions) and a citation network.The data is generated from all LaTeX sources on <a href="https://arxiv.org/">arXiv</a> and therefore of higher quality than data generated from PDF files.Typical uses are<ul><li>Training of ML models (citation recommendation, summarization, LLMs)</li><li>Citation context analysis</li><li>Bibliographic analyses</li></ul><h2>Access</h2>┏━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃  <a href="https://github.com/IllDepence/unarXive/raw/master/doc/unarXive_data_sample.tar.gz">D O W N L O A D   S A M P L E</a>   ┃ ┗━━━━━━━━━━━━━━━━━━━━━━━━━━┛Regarding the full data set, please note the following:<blockquote>Note: this Zenodo record is the "open subset" of unarXive, which contains all permissively licensed papers from arXiv.org. You can find the <a href="https://doi.org/10.5281/zenodo.7752754">full version here</a>.</blockquote>The code used for generating the data set is <a href="https://github.com/IllDepence/unarXive">publicly available</a>.

opencc-by-4.0Mar 2023View details →

Open Context Database SQL Dump: Legacy Schema Tables and New Schema Tables

Open Context (<a href="https://opencontext.org">https://opencontext.org</a>) publishes free and open access research data for archaeology and related disciplines. An open source (but bespoke) Django (Python) application supports these data publishing services. The software repository is here: <a href="https://github.com/ekansa/open-context-py">https://github.com/ekansa/open-context-py</a> The Open Context team runs ETL (extract, transform, load) workflows to import data contributed by researchers from various source relational databases and spreadsheets. Open Context uses PostgreSQL (<a href="https://www.postgresql.org">https://www.postgresql.org</a>) relational database to manage these imported data in a graph style schema. The Open Context Python application interacts with the PostgreSQL database via the Django Object-Relational-Model (ORM). In 2023, the Open Context team finished migration of from a legacy database schema to a revised and refactored database schema with stricter referential integrity and better consistency across tables. During this process, the Open Context team de-duplicated records, cleaned some metadata, and redacted attribute data left over from records that had been incompletely deleted in the legacy schema. This database dump includes all Open Context data organized with the legacy schema (table names that start with the 'oc_' or 'link_' prefixes) along with all Open Context data after cleanup and migration to the new database schema (table names that start with 'oc_all_'). The binary media files referenced by these structured data records are stored elsewhere. Binary media files for some projects, still in preparation, are not yet archived with long term digital repositories. These data comprehensively reflect the structured data currently published and publicly available on Open Context. Other data (such as user and group information) used to run the Website are not included.    IMPORTANT This database dump contains data from roughly 180 different projects. Each project dataset has its own metadata and citation expectations. If you use these data, you must cite each data contributor appropriately, not just this Zenodo archived database dump.

opencc-by-4.0Dec 2022View details →

Review of Open Call Record Datasets concerning the U.S. 911 Emergency Response System

The data available here identifies and describes a sampling of publicly available datasets about the 911 emergency response system. This list of datasets is a resource for researchers, civic technologists, activists, and journalists seeking to learn more about the 911 emergency response system. The list helps to identify relevant datasets that could be used to understand various types of 911 activity. During the first quarter of 2021, the R911 NAT created a list of priority cities including the top 100 cities by population, all state capitals, and the 82 cities that are home to Code for America Brigades. The team then conducted internet searches for each city using terms like “911 calls for service” and “open 911 data.” The dataset and a codebook defining each of these fields are provided as .csv files within a zip file. Note: this file does not contain the actual 911 datasets, which often number in the millions of records. The data_link field contains the URL of the site where each dataset is publicly available. See also: The Reimagine 911 knowledge base at: <a href="https://reimagine-911.gitbook.io/knowledge-base">https://reimagine-911.gitbook.io/knowledge-base</a> Contributors: This open data review was performed by the Code for America Reimagine 911 National Action Team. Contributing team members include: Aleks Hatfield, Brandon Bolton, Chizo Nwagwu, Dan Stormont, Elaine Chow, Em Spalti, Erica Pauls, Gio Sce, Gregory Janesch, Iva Momcheva, Ivelina Momcheva, Jamie Klenetsky Fay, Jason Trout, Jaya Prasad Jayakumar, Jennifer Miller, Jim Grenadier, Joanna Smith, Jonathan Melvin, Katlyn McGraw, Margaret Fine, Mariah Lynch, Micah Mutrux, Michelle Hoogenhout, Patina Herring, Peter Zeglen, Sarah Graham, Sebastian Barajas

opencc-zeroMar 2023View details →

Eusocial evolution without a nest: kin structure of social aphids forming open colonies on bamboo

Living in nests is an almost universal feature of eusocial animals. In some aphids, however, sterile soldier castes have evolved in open colonies without a nest. To clarify the factors promoting the evolution of eusociality in these colonies, we used newly developed microsatellite markers to compare the kin structure of the open colonies of two aphid species on bamboo: the non-eusocial colonies of Astegopteryx bambucifoliae and the eusocial colonies of Pseudoregma alexanderion Dendrocalamus latiflorus. Our samples, from over 1,000 hectares, contained 99 clones of A. bambucifoliae and 19 of P. alexanderi. Clonal mixing occurred in both species: average pairwise relatedness within a colony was 0.54 in A. bambucifoliae and 0.71 in P. alexanderi. Each clone of A. bambucifoliae occurred in a unique location, whereas those of P. alexanderi occurred in multiple locations and more than 90% of individuals came from just four clones. There was significant genetic variation among different colonies in the same clump (stem-cluster) in A. bambucifoliae but not in P. alexanderi, indicating that P. alexanderi colonies in a single clump are genetically homogenized, functioning as a large colony. In P. alexanderi, the proportion of sterile soldiers to normal first-instar nymphs was significantly different across the four clones. Our results indicate that the lack of input of migrants from the primary host and feeding on a large, stable host plant are important ecological factors that might favour the evolution of eusociality, enabling the production of genetically homogenised, large, and long-lived colonies. After eusociality evolves on the secondary host, the optimal strategy of soldier production might vary between different clones.

opencc-by-4.0Feb 2023View details →

Open dataset of 10% gelatin penetration experiments and simulation code for 4.5 and 6.35 mm caliber

Paper 1: PENETRATION EXPERIMENTS AND 1D SIMULATIONS OF AIR RIFLE BB 4.5 MM STEEL SPHERE AND GAMO HUNTER 4.5 MM IMPACTING 10% GELATINE Keywords: Penetration, experiments, simulations, gelatine, air rifle, projectiles, high-speed camera, chronograph, BB 4.5 mm, steel sphere, Gamo Hunter 4.5 mm, penetration depth, dynamic cavity size, drag force, shear force, shear rate effect Abstract. Gelatine of 10% concentration is often used as projectile target to simulate soft tissues of animals and humans. The 10% gelatine used in the tests fulfills the FBI standard protocol for penetration depth of BB 4.5 mm steel sphere impacting with 180 m/s. Here, experiments were conducted with BB 4.5 mm steel sphere and diabolo Gamo Hunter 4.5 mm pellets with varying impact velocity. The impact velocity was measured by chronograph. The deceleration and dynamic cavity size was studied by using high-speed camera with 10000 frames per second. Final penetration depth was manually measured. A 1D simulation model, considering the retardation force generated by drag and shear, was used to predict penetration depth in both 10% and 20% gelatine for projectiles with spherical nose shape. From the simulations it becomes evident that the drag force and static shear force alone can’t explain the total retardation force to achieve the expected penetration depth. In the literature for experiments conducted on both 10% and 20% gelatine, there is confirmation that projectiles impacting with velocity above 100 m/s, the shear strength in the gelatine is increased by a factor 40 and 70 times for 10% and 20% gelatine, respectively. This concept was successfully used in the simulations by introducing a shear rate dependent shear force model which increases the static shear force of 10% and 20% gelatine. All experimental results, including high speed films and python simulation code of gelatine penetration, are publicly available, see [1], [2].   Paper 2: Penetration experiments of air rifle projectiles with caliber 6.35 mm and different nose shapes impacting 10% gelatinE Keywords: Penetration, experiments, gelatine, air rifle, projectiles, high speed camera, chronograph, caliber 6.35 mm, H&N pellets, penetration depth, dynamic cavity size Abstract. Air rifles in caliber 6.35 mm and more than 10 J in kinetic energy at impact can have a significant effect on soft tissues of animals and humans. To study the effect, experimental penetration studies have been conducted by using test specimens made of 10% gelatine substitute. The 10% gelatine used in the tests fulfilled the FBI standard protocol for penetration depth of 4.5 mm BB steel sphere impacting with 180 m/s. The deceleration, penetration depth, and dynamic penetration cavity size for the projectiles with different nose shapes impacting gelatine 10% have been studied. The impact velocity was measured by using a chronograph and the initial kinetic energy before impact of the projectiles was up to 84 J (330 m/s). The deceleration and dynamic cavity size was studied by using high-speed camera with 10000 frames per second. Final penetration depth was manually measured. The nose and projectile shape influenced the dynamic cavity size and final penetration depth in the gelatine to a large extent. All experimental results, including high speed films and python simulation code of gelatine penetration, are publicly available, see [1].   Any results used from this open access data shall be cited to paper 1 and paper 2, the papers are found in the proceedings of the 14th International Conference on Shock & Impact Loads on Structures, 30-31 March 2023, Singapore.

opencc-by-4.0Feb 2022View details →

CES Collections in the UC Open Access Repository: 2021

This is a test file.

CCG: Beyond the Dams: Combatting Hydropower Over-reliance & Securing Pathways for a Low-carbon Future for Laos' Electricity Sector using OSeMOSYS (Open-Source Energy Modelling System)

Seven clicSAND scenario files for Beyond the Dams: Combatting Hydropower Over-reliance & Securing Pathways for a Low-carbon Future for Laos' Electricity Sector using OSeMOSYS (Open-Source Energy Modelling System).  How to Visualise Results Online and Offline outline the steps required to re-run the scenarios on OSeMOSYS Cloud Scenario Short Note outlines the steps to replicate the analysis and rebuild the scenarios Annex - Input Data and Assumptions listing the data sources and assumptions in the scenarios

opencc-by-4.0Nov 2022View details →

A comprehensive open-access database of electron backscattering coefficients for energies ranging from 0.1 KeV to 15 MeV

The database provides measured values of electron backscattering coefficient for 50 elements and 19 compounds at electron energies from 0.1keV to 15MeV.

opencc-zeroApr 2023View details →

General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive species in environmental samples. Continuous improvements in the method and the advances in sequencing platforms over the last decade have meant this approach is now widely used in biodiversity sciences and biomonitoring. For its general use, the method hinges on a correct identification of taxa. However, past studies have shown how this crucially depends on important decisions during sampling, sample processing, and subsequent handling of sequencing data. With no clear consensus as to the best practice, particularly the latter has led to varied bioinformatic approaches and recommendations for data preparation and taxonomic identification. In this study, using a large freshwater fish eDNA sequence dataset, we compared the frequently used zero-radius Operational Taxonomic Unit (zOTUs) approach of our raw reads and assigned it taxonomically i) in combination with publicly available reference sequences (open databases) or ii) with an OSU (Operational Sequence Units) database approach, using a curated database of reference sequences generated from specimen barcoding (closed database). We show both approaches gave comparable results for common species. However, the commonalities between the approaches decreased with read abundance and were thus less reliable and not comparable for rare species. The success of the zOTU approach depended on the suitability, rather than the size, of a reference database. Contrastingly, the OSU approach used reliable DNA sequences and thus often enabled species-level identifications, yet this resolution decreased with the recent phylogenetic age of the species. We show the need to include target group coverage, outgroups and full taxonomic annotation in reference databases to avoid misleading annotations that can occur when using short amplicon sizes as commonly used in eDNA metabarcoding studies. Finally, we make general suggestions to improve the construction and use of reference databases for metabarcoding studies in the future.

Over and Under Sampled Data-sets of Code Issues in Java Open-Source Projects

The dataset comprises code changes made to 15 Java Open-Source projects, classified with sentiment values (0 for negative and 1 for positive) based on developer reviews during various revision submissions. The dataset is available in 8 versions, each containing a sampled dataset using an over or under-sampling technique.

Open data and research tools

From article: Government Innovation Laboratories in South America: Congruences and Peculiarities Journal: Brazilian Administration Review (BAR)

Open metadata of the Institutional Repository (O2) of the UOC (Dataset in English)

<pre>Dataset of the metadata of all the academic and scientific production generated by the university community of the UOC.</pre>

Workflow for structured literature reviews using the Open Research Knowledge Graph (ORKG)

Figure showing a workflow of making a structured literature review using the core features of the Open Research Knowledge Graph (ORKG).

opencc-zeroApr 2023View details →

Data for: Integrated multi-trophic aquaculture with sugar kelp and oysters in a shallow coastal salt pond and open estuary site

The data set includes environmental data as well as kelp and oyster data from an integrated multi-trophic aquaculture study where sugar kelp was planted on four established oyster farms in Rhode Island, USA over 2 growing seasons (Year 1 = 2017-2018; Year 2 = 2018-2019). At each site, we planted to 60 m kelp lines (denoted as Line 1 and Line 2) approximately three weeks apart to determine optimal planting time. Kelp blade length and width was recorded at periodic intervals, and tissues were collected for carbon, nitrogen, δ15N, and δ13C analyses. Oyster growth data was collected from the same sites across the same timespans. Environmental data includes data collected on monthly farm visits with a YSI Sonde, as well as dissolved nutrients in the seawater. In addition, temperatures were logged on kelp lines every 15 minutes during each growing season.

Data set: The opening dynamics of the lateral gate regulates the activity of rhomboid proteases

Dataset: The opening dynamics of the lateral gate regulates the activity of rhomboid proteases Input: MD simulations + docking results

opencc-by-4.0Jan 2022View details →

Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

The Drug-Gene Interaction Database (DGIdb, <a href="http://www.dgidb.org/">www.dgidb.org</a>) is a web resource that provides information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data are normalized and merged into conceptual groups. The information contained in this resource is available to users through a straightforward search interface, an application programming interface (API), and TSV data downloads. DGIdb 4.0 is the latest major version release of this database. A primary focus of this update was integration with crowdsourced efforts, leveraging the Drug Target Commons for community-contributed interaction data, Wikidata to facilitate term normalization, and export to NDEx for drug-gene interaction network representations. Seven new sources have been added since the last major version release, bringing the total number of sources included to 41. Of the previously aggregated sources, 15 have been updated. DGIdb 4.0 also includes improvements to the process of drug normalization and grouping of imported sources. Other notable updates include the introduction of a more sophisticated Query Score for interaction search results, an updated Interaction Score, the inclusion of interaction directionality, and several additional improvements to search features, data releases, licensing documentation and the application framework.