scholarly journals Find research data repositories for the humanities - the data deposit recommendation service

2021 ◽  
Author(s):  
Stefan Buddenbohm ◽  
Maaike de Jong ◽  
Jean-Luc Minel ◽  
Yoann Moranville
Keyword(s):  
Research Data ◽  
Legal Requirements ◽  
Research Project ◽  
Data Repositories ◽  
Specific Research ◽  
Link Type ◽  
Set Up

AbstractHow can researchers identify suitable research data repositories for the deposit of their research data? Which repository matches best the technical and legal requirements of a specific research project? For this end and with a humanities perspective the Data Deposit Recommendation Service (DDRS) has been developed as a prototype. It not only serves as a functional service for selecting humanities research data repositories but it is particularly a technical demonstrator illustrating the potential of re-using an already existing infrastructure - in this case re3data - and the feasibility to set up this kind of service for other research disciplines. The documentation and the code of this project can be found in the DARIAH GitHub repository: https://dariah-eric.github.io/ddrs/.

scholarly journals GenIE-Sys: Genome Integrative Explorer System

2019 ◽  
Author(s):  
Chanaka Mannapperuma ◽  
John Waterworth ◽  
Nathaniel Street
Keyword(s):  
Source Code ◽  
Genome Project ◽  
Data Repositories ◽  
Web Resources ◽  
Link Type ◽  
Maximum Benefit ◽  
A Genome ◽  
Set Up ◽  
User Friendly ◽  
Mining Tools

AbstractThere are an ever-increasing number of genomes being sequenced, many of which have associated RNA sequencing and other genomics data. The availability of user-friendly web-accessible mining tools ensures that these data repositories provide maximum benefit to the community. However, there are relatively few options available for setting up such standalone frameworks. We developed the Genome Integrative Explorer System (GenIE-Sys) to set up web resources to enable search, visualization and exploration of genomics data typically generated by a genome project.GenIE-Sys is implemented in PHP, JavaScript and Python and is freely available under the GNU GPL 3 public license. All source code is freely available at the GenIE-Sys website (https://geniesys.org) or GitHub (http://github.com/plantgenie/geniesys.git). Documentation is available at http://geniesys.readthedocs.io.

scholarly journals Development, piloting, and evaluation of an evidence-based informed consent form for total knee arthroplasty (EvAb-Pilot): a protocol for a mixed methods study

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Alina Weise ◽  
Julia Lühnen ◽  
Stefanie Bühn ◽  
Felicia Steffen ◽  
Sandro Zacher ◽  
...  
Keyword(s):  
Total Knee Arthroplasty ◽  
Informed Consent ◽  
Adverse Events ◽  
Knee Arthroplasty ◽  
Evidence Based ◽  
Nocebo Effect ◽  
Legal Requirements ◽  
Consent Forms ◽  
Link Type ◽  
Total Knee

Abstract Background Practitioners frequently use informed consent forms to support the physician-patient communication and the informed consent process. Informed consent for surgery often focuses on risk centered information due to high liability risks for treatment errors. This may affect patients’ anxiety of adverse events and the nocebo effect. This study focuses on the optimization of pre-surgical information on risks and complications, and at the same time reconciles these information with legal requirements. Methods The development, piloting, and evaluation of evidence-based informed consent forms for total knee arthroplasty (TKA) and related anesthesia procedures will follow the UK MRC Framework for developing and evaluating complex interventions. Conducting different sub-studies, we will (I) qualitatively explore the information acquisition and decision-making processes, (II) develop and pilot test evidence-based informed consent forms on the example of TKA and related anesthesia procedures, (III) conduct a monocentric interrupted time series (ITS) pilot study to evaluate the effects of evidence-based informed consent forms in comparison with standard consent forms, and (IV) perform a process evaluation to identify barriers and facilitators to the implementation of the intervention and to analyze mechanisms of impact. Discussion The evidence-based and understandable presentation of risks in informed consent forms aims at avoiding distorted risk depiction and strengthening the patients’ competencies to correctly assess the risks of undergoing surgery. This might reduce negative expectations and anxiety of adverse events, which in turn might reduce the nocebo effect. At the same time, the practitioners’ acceptance of evidence-based informed consent forms meeting legal requirements could be increased. Trial registration ClinicalTrials.gov, NCT04669483. Registered 15 December 2020. German Clinical Trials Registry, DRKS00022571. Registered 15 December 2020

scholarly journals Collaborative research and knowledge translation on road crashes in Burkina Faso: the police perspective 18 months on

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Christian Dagenais ◽  
Michelle Proulx ◽  
Esther Mc Sween-Cadieux ◽  
Aude Nikiema ◽  
Emmanuel Bonnet ◽  
...  
Keyword(s):  
Knowledge Translation ◽  
Burkina Faso ◽  
Road Traffic ◽  
Research Data ◽  
Road Traffic Crash ◽  
Research Project ◽  
Traffic Crashes ◽  
Road Traffic Crashes ◽  
Road Crashes

AbstractIn this commentary, we present a follow-up of two articles published in 2017 and 2018 about road traffic crashes, which is an important public health issue in Africa and Burkina Faso. The first article reported on a research project, conducted in partnership with local actors involved in road safety, carried out in Ouagadougou in 2015. Its aim was to test the effectiveness, acceptability, and capacity of a surveillance system to assess the number of road traffic crashes and their consequences on the health of crash victims. Several knowledge translation activities were carried out to maximize its impact and were reported in the 2018 article published in HRPS: monthly reports presenting the research data, large-format printed maps distributed to the city’s police stations, and a deliberative workshop held at the end of the research project. The present commentary presents our efforts to deepen our understanding of the impacts of the knowledge translation strategy, based on follow-up interviews, 18 months after the workshop, with the heads of the road traffic crash units in Ouagadougou police stations (n = 5). Several benefits were reported by respondents. Their involvement in the process prompted them to broaden their knowledge of other ways of dealing with the issue of road crashes. This led them, sometimes with their colleagues, to intervene differently: more rapid response at collision sites, increased surveillance of dangerous intersections, user awareness-raising on the importance of the highway code, etc. However, sustaining these actions over the longer term has proven difficult. Several lessons were derived from this experience, regarding the importance of producing useful and locally applicable research data, of ensuring the acceptability of the technologies used for data collection, of using collaborative approaches in research and knowledge translation, of ensuring the visibility of actions undertaken by actors in the field, and of involving decision-makers in the research process to maximize its impacts.

Improvements for research data repositories: The case of text spam

2021 ◽  
pp. 016555152199863
Author(s):  
Ismael Vázquez ◽  
María Novo-Lourés ◽  
Reyes Pavón ◽  
Rosalía Laza ◽  
José Ramón Méndez ◽  
...  
Keyword(s):  
Web Application ◽  
Research Data ◽  
Data Sets ◽  
Data Repositories ◽  
Software Applications ◽  
Public Data ◽  
Protection Mechanisms ◽  
Experimental Protocols ◽  
Learning Research ◽  
Processing Steps

Current research has evolved in such a way scientists must not only adequately describe the algorithms they introduce and the results of their application, but also ensure the possibility of reproducing the results and comparing them with those obtained through other approximations. In this context, public data sets (sometimes shared through repositories) are one of the most important elements for the development of experimental protocols and test benches. This study has analysed a significant number of CS/ML ( Computer Science/ Machine Learning) research data repositories and data sets and detected some limitations that hamper their utility. Particularly, we identify and discuss the following demanding functionalities for repositories: (1) building customised data sets for specific research tasks, (2) facilitating the comparison of different techniques using dissimilar pre-processing methods, (3) ensuring the availability of software applications to reproduce the pre-processing steps without using the repository functionalities and (4) providing protection mechanisms for licencing issues and user rights. To show the introduced functionality, we created STRep (Spam Text Repository) web application which implements our recommendations adapted to the field of spam text repositories. In addition, we launched an instance of STRep in the URL https://rdata.4spam.group to facilitate understanding of this study.

scholarly journals Clinical and multi-omics cross-phenotyping of patients with autoimmune and autoinflammatory diseases: the observational TRANSIMMUNOM protocol

BMJ Open ◽  
2018 ◽  
Vol 8 (8) ◽  
pp. e021037 ◽  
Author(s):  
Roberta Lorenzon ◽  
Encarnita Mariotti-Ferrandiz ◽  
Caroline Aheng ◽  
Claire Ribet ◽  
Ferial Toumi ◽  
...  
Keyword(s):  
Systems Biology ◽  
Good Clinical Practice ◽  
Autoinflammatory Diseases ◽  
Case Report Form ◽  
Sample Collection ◽  
Clinical Protocol ◽  
Link Type ◽  
Systems Immunology ◽  
Hospital Ethics ◽  
Set Up

IntroductionAutoimmune and autoinflammatory diseases (AIDs) represent a socioeconomic burden as the second cause of chronic illness in Western countries. In this context, the TRANSIMMUNOM clinical protocol is designed to revisit the nosology of AIDs by combining basic, clinical and information sciences. Based on classical and systems biology analyses, it aims to uncover important phenotypes that cut across diagnostic groups so as to discover biomarkers and identify novel therapeutic targets.Methods and analysisTRANSIMMUNOM is an observational clinical protocol that aims to cross-phenotype a set of 19 AIDs, six related control diseases and healthy volunteers . We assembled a multidisciplinary cohort management team tasked with (1) selecting informative biological (routine and omics type) and clinical parameters to be captured, (2) standardising the sample collection and shipment circuit, (3) selecting omics technologies and benchmarking omics data providers, (4) designing and implementing a multidisease electronic case report form and an omics database and (5) implementing supervised and unsupervised data analyses.Ethics and disseminationThe study was approved by the institutional review board of Pitié-Salpêtrière Hospital (ethics committee Ile-De-France 48–15) and done in accordance with the Declaration of Helsinki and good clinical practice. Written informed consent is obtained from all participants before enrolment in the study. TRANSIMMUNOM’s project website provides information about the protocol (https://www.transimmunom.fr/en/) including experimental set-up and tool developments. Results will be disseminated during annual scientific committees appraising the project progresses and at national and international scientific conferences.DiscussionSystems biology approaches are increasingly implemented in human pathophysiology research. The TRANSIMMUNOM study applies such approach to the pathophysiology of AIDs. We believe that this translational systems immunology approach has the potential to provide breakthrough discoveries for better understanding and treatment of AIDs.Trial registration numberNCT02466217; Pre-results.

scholarly journals GAMS – An infrastructure for the long-term preservation and publication of research data from the Humanities

2018 ◽  
Vol 71 (1) ◽  
pp. 207-216 ◽  
Author(s):  
Johannes Hubert Stigler ◽  
Elisabeth Steiner
Keyword(s):  
System Architecture ◽  
Academic Research ◽  
Research Data ◽  
Data Repository ◽  
Data Repositories ◽  
Domain Specific ◽  
Preservation Policy ◽  
Long Term Preservation ◽  
Data Centres

Research data repositories and data centres are becoming more and more important as infrastructures in academic research. The article introduces the Humanities’ research data repository GAMS, starting with the system architecture to preservation policy and content policy. Challenges of data centres and repositories and the general and domain-specific approaches and solutions are outlined. Special emphasis lies on the sustainability and long-term perspective of such infrastructures, not only on the technical but above all on the organisational and financial level.

scholarly journals Using playful methods to understand children’s digital literacies

2021 ◽  
Author(s):  
Pekka Mertala
Keyword(s):  
Digital Literacy ◽  
Research Data ◽  
Research Approach ◽  
Research Projects ◽  
Digital Literacies ◽  
Research Project ◽  
Childhood Education ◽  
Context Sensitive ◽  
The Individual ◽  
Meaningful Research

This chapter is the final for Section 3 and in many ways stands as an example of how many of the individual elements presented thus far in the book, can come together in a holistic way. This chapter demonstrates how we can adopt play, make it unique to the project and the children and still arrive at meaningful research data. This chapter describes a research project wherein 3- to 6-year-old Finnish children’s digital literacies were studied and supported via playful methods. The key theses this chapter advocates are:-The use of playful methods in early childhood education (ECE) research is one way to acknowledge and respect the characteristics of the research context.-The ambiguity of play should be acknowledged when planning, conducting, and evaluating playful research projects.-Studying and supporting children’s digital literacies do not always require digital devices.The chapter is structured as follows. First, a reflective discussion on the ambiguity of play and the use of playful methods as a context-sensitive research approach is presented. Then, an overview of the research project and its objectives are provided. In the end, three concrete examples of how the children’s digital literacy was studied and supported using playful methods are given.

scholarly journals Connecting Data Publication to the Research Workflow: A Preliminary Analysis

2017 ◽  
Vol 12 (1) ◽  
pp. 88-105 ◽  
Author(s):  
Sünje Dallmeier-Tiessen ◽  
Varsha Khodiyar ◽  
Fiona Murphy ◽  
Amy Nurnberger ◽  
Lisa Raymond ◽  
...  
Keyword(s):  
Working Group ◽  
Research Data ◽  
Data Publishing ◽  
Data Repository ◽  
Research Activity ◽  
Data Repositories ◽  
Data Publication ◽  
Loosely Coupled ◽  
Definition Of ◽  
Data Documentation

The data curation community has long encouraged researchers to document collected research data during active stages of the research workflow, to provide robust metadata earlier, and support research data publication and preservation. Data documentation with robust metadata is one of a number of steps in effective data publication. Data publication is the process of making digital research objects ‘FAIR’, i.e. findable, accessible, interoperable, and reusable; attributes increasingly expected by research communities, funders and society. Research data publishing workflows are the means to that end. Currently, however, much published research data remains inconsistently and inadequately documented by researchers. Documentation of data closer in time to data collection would help mitigate the high cost that repositories associate with the ingest process. More effective data publication and sharing should in principle result from early interactions between researchers and their selected data repository. This paper describes a short study undertaken by members of the Research Data Alliance (RDA) and World Data System (WDS) working group on Publishing Data Workflows. We present a collection of recent examples of data publication workflows that connect data repositories and publishing platforms with research activity ‘upstream’ of the ingest process. We re-articulate previous recommendations of the working group, to account for the varied upstream service components and platforms that support the flow of contextual and provenance information downstream. These workflows should be open and loosely coupled to support interoperability, including with preservation and publication environments. Our recommendations aim to stimulate further work on researchers’ views of data publishing and the extent to which available services and infrastructure facilitate the publication of FAIR data. We also aim to stimulate further dialogue about, and definition of, the roles and responsibilities of research data services and platform providers for the ‘FAIRness’ of research data publication workflows themselves.

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