Find research datasets worth reusing

A Versatile and Secure Data Management System API facilitating the Interconnection of any software component and Easy Data Access.

In the context of the EU-funded project PILOTING (No. 871542), a versatile Data Management System (DMS) was deployed and facilitated the easy integration of nine different robotic systems and various payloads and the storing of all the data observations produced during the inspections. The DMS is designed under the DMS-Data Model (DMS-DM) and operates on top of a representational state transfer (REST) application programming interface (API) that provides a simplified way to exchange data through HTTP(S) requests from a client to the server. One of its key advantages is that it provides a great deal of flexibility so the model could accommodate extensions if needed. Data is not tied to resources or methods, so REST can handle multiple types of calls, return different data formats and even change structurally with the correct implementation of hypermedia.  It supports CRUD operations via GET, POST, PUT, PATCH, and DELETE HTTP methods and stores the data on a PostgreSQL object-relational database system. The REST API has been created with Python's Django (web framework) and Django REST Framework, a powerful and flexible toolkit for building Web APIs.  The constructed document presents the communication endpoints (DMS API’s Uniform Resource Identifiers (URIs)) under which an authorized user can have access to the DMS API and subsequently to the collected data.

opencc-zeroDec 2022View details →

dryad36/100

Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions

Medicago truncatula is a model legume that has been extensively investigated in diverse subdisciplines of plant science. Medicago littoralis can interbreed with M. truncatula and M. italica; these three closely related species form a clade, i.e. TLI clade. Genetic studies have indicated that M. truncatula accessions are heterogeneous, but their taxonomic identities have not been verified. To elucidate the phylogenetic position of diverse M. truncatula accessions within the genus, we assembled 54 plastid genomes (plastomes) using publicly available next-generation sequencing data and conducted phylogenetic analyses using maximum likelihood. Five accessions showed high levels of plastid DNA polymorphism. Three of these highly polymorphic accessions contained sequences from both M. truncatula and M. littoralis. Phylogenetic analyses of sequences placed some accessions closer to distantly related species suggesting misidentification of source material. Most accessions were placed within the TLI clade and maximally supported the interrelationships of three subclades. Two Medicago accessions were placed within a M. italica subclade of the TLI clade. Plastomes with a 45-kb (rpl20-ycf1) inversion were placed within the M. littoralis subclade. Our results suggest that the M. truncatula accession genome pool represents more than one species due to possible mistaken identities and gene flow among closely related species.

Digital Community Heritage and Open Access Dataset

Dataset containing 27 digital community heritage initiatives, defined as online initiatives where community members or users contribute to a community heritage-related common cause, which promotes the interests of the community(ies) and/or the greater public. Access the report: Ziku, M., & Fabos, B. (2022). Digital Community Heritage and Open Access. CC Open Culture Working Group Digital Community Heritage. https://doi.org/10.21428/9eb74dbf.0c46e6be

opencc-by-4.0Dec 2022View details →

Web Accessibility Evaluation Data - March to September 2021

This dataset contains the dump of a PostgreSQL database with the contents of automated web accessibility evaluation of nearly 3 million webpages obtained with QualWeb between March and September 2021.

opencc-by-4.0Jan 2023View details →

Armony Altinier: What Does Green Digital Accessibility Mean to You?

In this video Dr. Armony Altinier, co-founder of Koena shares her opinion on green digital accessibility.

opencc-by-4.0Jan 2023View details →

Gert Vercauteren: What Does Green Digital Accessibility mean to you?

Tenure Track Professor Gert Vercauteren from University of Antwerp shares his thoughts on the concept of Green Digital Accessibility.

dryad36/100

Dataset associated with the manuscript: Soil management legacy interacts with wheat genotype to determine access to organic N in a dryland system

Organic nutrient management through the application of compost and/or cover crops provides mineralizable sources of nutrients for plants while often building soil organic matter (SOM) and various aspects of soil health. Variability in nutrient acquisition strategies between crop genotypes may confer advantages under different soil health contexts and could be important for crop selection and breeding, but crop response under field conditions remains unexplored. We investigated the ability of different genotypes of winter wheat (Triticum aestivum L.) to access nitrogen (N) from newly added cover crop residues in two soils with contrasting levels of SOM and biological activity. We planted three previously characterized wheat genotypes in a long-term dryland compost amendment field trial: 1) Byrd (modern, deep roots, low exudation), 2) Cheyenne (historic, drought susceptible, intermediate exudation), and 3) Snowmass (modern, drought-susceptible, high exudation). 15N-labelled cover crop residue was added to each plot and traced into wheat tissue. In the low SOM soil, the high exudate genotype Snowmass and historic genotype Cheyenne took up the most residue-derived N (6.4-8.1 kg N ha-1) compared to the low-exudate genotype Byrd (4.4 kg N ha-1), suggesting a strong exudate effect in the more carbon-limited soil. However, the low-exudate, deep rooted genotype, Byrd, took up the most residue N in the high SOM soils (4.6 kg N ha-1 vs. 2.8 and 3.3 hg N ha-1 for Cheyenne and Snowmass, respectively), which indicated higher native N cycling activities and great importance of drought resistance. Enzyme activity, inorganic N, and microbial communities were not influenced by genotype, though did show strong effects of compost application legacy. Our results show that belowground allocation strategies that favor microbial stimulation may be less successful under water limitation, especially when high SOM can support mineralization of residue N without added investment in root inputs. Increased soil health through SOM-building management likely enhances nutrient cycling, and may better support root strategies that invest less in microbial stimulation in favor of other limiting resources.

opencc-zeroJan 2023View details →

opencc-by-4.0Dec 2022View details →

Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)"

Abstract: Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardised sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, in order to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little studied region but an important biodiversity hotspot, complete mitochondrial genomes and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analysed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, Cirripectes castaneus, C. randalli, and C. stigmaticus. C. castaneus and C. stigmaticus both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, C. randalli shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of C. castaneus, C. randalli and C. stigmaticus in Rodrigues, and the presence of C. stigmaticus in Reunion. This study contributes to fill the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g. eDNA). Content of this repository: Genbank and BOLD accession numbers of sequences from "New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)" published in Ecology and Evolution (2023)

opencc-by-4.0Sep 2022View details →

Choosing Open Access Publishing: The Key Issues

In this interactive webinar aimed at PhD students, post-docs and other early career researchers, Professor Patrick Dunleavy and Dr Frances Pinter introduced participants to Open Access Book Publishing, answered questions concerning the current publishing landscape, and gave insight into career-related issues for junior researchers to consider when choosing to publish open access. Although aimed specifically at junior researchers, this online webinar was open to all who wished to participate from across the CIVICA partner institutions.

opencc-by-4.0Feb 2023View details →

SWDA Inequalities Dataset: Safe Water Drinking Water Access Indicator and Inequalities Indexes of Brazilian Municipalities

The SWDA Inequalities Dataset consist on results of Safe Drinking Water Access - SDWA indicators and inequalities indexes obtained by an adapted Lorenz Curve approach calculated for all Brazilian municipalities.The main datasource is the Brazillian 2010 Demographic Census, which is the last Population Census data publicaly available. The SDWA indicators are weighted by the SDWA values corresponding to census tracts considering permanent private household residents (Eq. 2). The safe drinking water sources are: (i) general water distribution network; (ii) well or spring located on the property; (iii) rainwater stored in a cistern, cement box, etc.; (iv) or well or spring outside the property, tank car, rainwater stored otherwise, river, dam, lake or stream, or another form of water supply. Considering that these drinking water sources differ in terms of accessibility, availability and water quality, the AHP Method was applied to obtain different weights for each form of water access (Eq. 1). The Gini Index (G_water), Concentration Coefficient (C_water) and Dissimilarity Index (D_water), were adapted to analyze inequalities in SDWA. The Safe Drinking Water Concentration Index is obtained from the Lorenz Curve, with the percentage of residents in permanent households accumulated and ordered by per capita income in the abscissa of the graph (Eq. 3). The per capita income is obtained by the ratio between the total nominal monthly income and the number of residents of the permanent households of each census tract. The Safe Drinking Water Gini Index was similarly adapted, with the residents accumulated and ordered by the safe drinking water rate in the abscissa of the graph (Eq. 4).  The ratios between Upper and Lower Quintiles (R_8020) were obtained for each municipality, that is, the relationship between the rates of SDWA for permanent private households that represent 20% of the residents with the highest average per capita income (4th quintile represented by Q4) and the most economically unfavorable 20% (1st quintile represented by Q1) (Eq. 5). The Safe Drinking Water Dissimilarity Index is calculated by the weighted average of the absolute difference of the SDWA indicator of each quintile of the average per capita income and the average rate (Eq. 6). The inequalities indexes are also presented as normalized values (G_water_norm, C_water_norm, R_8020_norm, D_water_norm). \(t_{water} = 0.376*t_{piped} + 0.309*t_{well} + 0.274*t_{cistern} + 0.041*t_{others} \;\;\;\;\;\;\;\;\;\; (Eq. 1) \) \(0.041 \leq t_{water} \leq 0.368\) \(t_{piped} + t_{well} + t_{cistern} + t_{others} = 1\) t is the relationship between residents in permanent private households with access (piped, well, cistern and/or other) and the total number of residents in permanent private households. \(SDWA = \frac{\sum_{i=1}^{n} (t_{water_{norm_i}}*p_i)}{\sum_{i=1}^{n}(p_i)} \;\;\;\;\;\;\;\;\;\; (Eq. 2)\) considering the percentage of residents in permanent private households of each sector (pi) and the number of census tracts (n). \(C_{water} = (p_{r_i}*t_{water_{norm_{i+1}}} - p_{r_{i+1}}*t_{water_{norm_{i}}}) + ... + (p_{r_{i-1}}*t_{water_{norm_{i}}} - p_{r_i}*t_{water_{norm_{i-1}}}) \;\;\;\;\;\;\;\;\;\; (Eq. 3)\) where \(p_{r_i}\) stand for a percentage of residents in permanent private households ordered by average income per capita, with Cwater ranging between -1 and 1. \(G_{water} = 1 - {\sum_{i=1}^{n}(p_{w_i}-p_{w_{i-1}})*(t_{water_{norm_i}} + t_{water_{norm_{i-1}}}}) \;\;\;\;\;\;\;\;\;\; (Eq. 4)\) where \(p_{w_i}\)  is the percentage of residents in permanent private households ordered by the weighted water access rate ( \(t_{water_{norm}}\)), and Gwater ranging between 0 and 1. \(R_{80/20} = \frac{t_{water_{norm_{Q_4}}}}{t_{water_{norm_{Q_1}}}} \;\;\;\;\;\;\;\;\;\; (Eq. 5)\) with R80/20 ranging between 0 and ∞. \(D_{water} = \frac{1}{2\overline t_{water_{norm}}} \times \sum_{i=1}^{n}\beta_i |t_{water_{norm_i}} - \overline t_{water_{norm}}| \{ \sum \beta_i = 1 \;\;\;\;\;\;\;\;\;\; (Eq. 6)\) with βi standing for the proportion of group i in the sample, \(\overline t_{water_{norm}}\)  the normalized mean safe drinking water access rate of the municipality, \(t_{water_{norm_i}}\) the normalized safe drinking water access rate of group i, with a value between 0 and 1; and n the number of groups (n= 5); with Dwater presenting values between 0 and 1.

Preparing your thesis for an Open Access Repository

The presenters gave participants a helpful overview prior to submitting their PhD thesis to LSE Theses Online and making it open access. Their presentation answered such questions as: <ul> <li>What do you need to know about using copyright material in your PhD thesis?</li> <li>How does making your PhD thesis available on LSETO benefit you?</li> <li>What are the implications for your publishing plans?</li> </ul>

opencc-by-4.0Jun 2022View details →

Open Language Access (OLA): Democratising Linguistic Resources

The audio file is a podcast introducing the Open Language Access (OLA) project. OLA is a collaborative digital archive that brings together researchers from all over the world. Launched in 2019 in the context of linguistic research, OLA is not just an archive but, above all, a platform that aims at providing tools for the creation, collaborative editing, exploration and publication of textual archives. In today's society, language stands as a central tool for change, and at the same time as a register and trace of the change itself. Hence the need to create a digital and accessible linguistic archive (open source and open access) with the aim of changing the paradigms of society's observation by providing an accessible tool to anyone who wants to look at change through language.

opencc-by-4.0Feb 2023View details →

Tampere - Urban green space accessibility and distribution

Results of the evaluation of urban green space accessibility and distribution in Vuores neighbourhood in Tampere.

Nipah virus: Analysis of the scientific production in Open Access on the Web of Science, 2000 - 2020

Data used in the analysis of the scientific production of Nipah in open access in the period 2000 to 2020

GEOLAB Transnational Access project RELERT - Risk and reliability study in quick clay

Quick clay is characterised by complete collapse and liquid-like mobility when overloaded. Quick clay is found primarily in Norway and Sweden, but also exists in Finland, Russia, Canada and Alaska. Quick clay landslides, with their retrogression characteristics and extreme mobility, pose significant risk to human lives, infrastructure, property and surrounding ecosystems. Hence, the proper characterization of quick clay sites is essential for ensuring the safety and resilience of infrastructure in Norway and elsewhere in Europe. The current practice for mapping quick clay in Norway relies heavily on borehole data with either rotary sounding or total sounding and core samples tested in the laboratory. The only method for identifying quick clay with certainty is physical testing in the laboratory, but it is time-consuming, expensive and gives limited information, i.e., only at the depths and locations where the sample is taken. In Norway, rotary sounding and total soundings are frequently used in mapping of quick clay. In addition, geophysical methods such as Electrical Resistivity Tomography (ERT) are also occasionally used to supplement the results from soundings, particularly in early stage of ground investigation. Rotary sounding is regarded as the most cost-effective method for detecting potentially quick clay pockets. The accuracy of quick clay mapping by a certain ground investigation method increases with increasing number of boreholes and decreasing distances to the boreholes in the area of interest. The accuracy is also increased with additional data sources such as ERT and/or other geophysical methods. Each rotary sounding, for example, provides information on the potential occurrence of quick clay with high accuracy at its location, but the accuracy decreases with increasing distance from the actual location of the rotary sounding. Current practice of mapping quick clay rarely deals with uncertainties associated with ground investigations quantitatively.  The uncertainties arise due to various sources including the interpretation of the rotary sounding, the number of soundings and the distance from the soundings, the equipment itself and the testing procedure. Dealing with uncertainty currently relies heavily on engineering judgement, which is subjective. Transnational Access project RELERT is funded through the 1st call for proposal for the GEOLAB project. This project aims at developing models and validated on results from field testing to deal with uncertainty in ground characterisation in quick clay area more quantitatively. The objectives of the RELERT project are: (i) to obtain and process ground investigation data profiles at the Tiller-Flotten quick clay site (i.e. rotary soundings and ERT (electrical resistivity tomography) profiles. Notes: some of the data reported is obtained in earlier field investigation campaign but are processed and reported in this projects. (ii) to build a mathematical model that characterizes the spatial variability of quick clays in Norway and (iii) to develop a methodology for reliability assessment of quick clay sites under retrogressive failure. We employ rotary soundings, soil samples and will use ERT-results in further study to learn the parameters of a hierarchical random field model, recently proposed by the user group for modelling the inherent spatial variability of material properties. The parameters of the model is learned by application of Bayesian analysis on the ground investigation data. In further studies, we plan to use the model in slope reliability assessments under retrogressive slope failure through application of Monte Carlo methods. The results of the study are and will be documented in joint publications of the host and user groups.

opencc-by-4.0Feb 2023View details →

Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in mice.

Raw reads for whole genome sequencing and RNAseq for Gellman et al., 2023.

Supplementary Online Content to "Alterity marking and enhancing accessibility in lexical borrowing: Meta-information techniques in the use of incipient anglicisms in French and Italian"

<ul> <li>Overview of newspaper articles analysed in Sections 4 and 5</li> <li>Sources of the newspaper articles</li> <li>Sample analyses of the use of meta-information techniques in F2 and I3</li> </ul>

Improving access and research infrastructure for the internet's images

Access to image-based resources is fundamental to research and the transmission of cultural knowledge. Digital access offers the potential for scholars to employ heritage collections internationally via the internet. However, most of the internet’s image-based resources have been locked up in silos, and access at resolutions useful for research has been restricted to bespoke, locally-built applications. The International Image Interoperability Framework (IIIF) can solve this problem using Application Program Interfaces (APIs) which allow images and metadata held in different digital collections to be accessed in a standardised format. In this EU-funded MUYA-IIIF project 694612 Proof of Concept project (the MUYA-IIIF PoC) the School of African and Oriental Studies (SOAS) has addressed the problem of tools and infrastructure to realize the potential of IIIF in practical workflows for researchers in the social sciences and humanities. Heretofore the large number of organizations worldwide now providing access to their image-based resources via IIIF have only supported viewing, and not the routine use of research processes such as standards-based scientific annotation. The MUYA-IIIF PoC has worked with the British Library (BL) and the hasdai Partnership of CERN and Data Futures GmbH to build and employ a general-purpose IIIF annotation workflow, extending existing research conducted under earlier The Multimedia Yasna ERC advanced grant. Significantly, not only have problems of annotation workflows been addressed by the MUYA-IIIF PoC, but also the creation of new, reusable primary data resources from research employing annotation, which can be preserved using the W3C's Web Annotation Data Model (WADM) standards and state-of-the art InvenioRDM repository technology. Specifically, MUYA-IIIF has annotated textual structure in key Avestan manuscripts from multiple collections, including from the British Library, to connect the digitized manuscript imagery with structured transcriptions of the text it bears, enabling analysis and searching. While many institutions internationally now provide IIIF data resources based on their manuscript collections, very few of these are yet compatible with standards-based annotation. The Oxford MA in digital scholarship found, as recently as Fall 2022, that it needed to convert libraries' IIIF resources before being able to annotate them. In contrast, MUYA-IIIF has produced a new WADM-compliant IIIF service, which can now be freely annotated by scholars, and it has also created annotations of all of the stanzas of the Zoroastrian Yasna ceremony. In turn, this has permitted reuse of existing research investment using Text Encoding Initiative (TEI) analysis of the Yasna. As a result a significant speed-up has been achieved in developing comprehensive interactive transcription of the Yasna manuscripts. The second part of the MUYA-IIIF project has addressed sustainability and reuse of this new digital collection: in contrast, many data resources in the Humanities and in cultural heritage become vulnerable to technology obsolescence. In particular, WADM annotations are stand-off in nature—they are stored separately from the digitized manuscript imagery and demand new approaches for effective preservation and accessibility for the wider research community. MUYA-IIIF has therefore worked with the hasdai partnership to gain access to new repository technology developed in the InvenioRDM consortium, which supports annotation. InvenioRDM is the software platform on which the upgrade of the European Commission's OpenAIRE trusted Zenodo repository is based. To support such long-term access and reuse, the project's outputs comprise four components, which together form a sustainable data resource on which not only SOAS but also the external research community can build. <ul> <li>the MUYA InvenioRDM corpus repository provides metadata linked to the British Library manuscript record, and a IIIF viewer for the BL Arundel Yasna manuscript imagery.</li> <li>annotations produced in the MUYA-IIIF project are available for download as a WADM. dataset—these annotations are linked to the manuscript imagery via Persistent IDentifiers (PIDs).</li> <li>the IIIF service for the manuscript is available for use by external IIIF applications and researchers' tools.</li> <li>a Zenodo record, linked to the corpus repository, provides the Yasna annotation collection dataset, and this is discoverable by international libraries via the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH).</li> </ul> The new MUYA InvenioRDM corpus repository is supported in the long-term through the hasdai Partnership, and the Zenodo record is supported by the EC's OpenAIRE program. In this way MUYA-IIIF has created a new sustainability benchmark for digital research investments using scientific annotation, by assembling standards-based infrastructures and making very long-term costs of operation of complex data resources forecastable in concrete terms. Implementation of the project The project was divided into work-packages, reflecting three main activities: <ul> <li>creating a IIIF service for the British Library Arundel manuscript of the Yasna ceremony and building an annotation workflow</li> <li>annotating the chapters and stanzas of the Yasna and connecting them with transcriptions and analyses already accomplished in other research activities</li> <li>developing a corpus repository for Zoroastrian manuscripts to support both accessibility for the research community and also preservation of the research investment in digitization and annotation, as well as connecting other existing research outcomes</li> </ul> The annotation workflow for the project employed the freizo anəstor platform developed by Data Futures GmbH and employed by institutions in Europe and the U.S. including CERN, Heidelberg, Oxford and Notre Dame, and this was configured for work on the Yasna manuscript. Anəstor can generate multiple versions of Open Annotation Data Model and Web Annotation Data Model (WADM) annotations, to address differences between existing, current and future standards-based WADM research environments, and it is being integrated with the Zenodo global catch-all repository of OpenAIRE. The annotation workflow provided security for SOAS scholars through ORCID authentication, so that their work was protected from unauthorized modification, and also allowed their contributions to be tracked and credited for citation. In addition the workflow exported annotation collections in a preservable form for efficient access by the research community and for preservation. Developing an InvenioRDM corpus repository for the MUYA-IIIF project enabled the digital version of the manuscript, together with the British Library metadata, to be presented without restrictions on the internet, and for the annotation collections to form a foundation for future research via down-loadable JSON datasets (JSON is technology-agnostic and can be employed by a wide range of current and future research software applications). SOAS now plans to extend the MUYA-IIIF repository with additional manuscripts based on fieldwork in India and Iran and through collaborations with other institutions worldwide. Long-term hosting of this data resource by the hasdai Partnership is already organized for 10 years and new developments such as the Oxford Common File Layout (OCFL) are enabling both very long-term preservation using LTO tape libraries and also cross repository interoperability for resilience as technologies continue to evolve.

opencc-by-4.0Feb 2022View details →

CES Collections in the UC Open Access Repository: 2021

This is a test file.

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.