Mapping variation in Basque: The BiV database

2019 ◽  
Vol 23 (2) ◽  
pp. 347-374
Author(s):  
Beatriz Fernández ◽  
Ane Berro ◽  
Iñigo Urrestarazu ◽  
Itziar Orbegozo
Keyword(s):  
Open Access ◽  
Research Group ◽  
Linguistic Variation ◽  
Online Database ◽  
Dialectal Variation ◽  
Fine Grained ◽  
User Friendly

Abstract The aim of this paper is to present the Euskara Bariazioan/Basque in Variation (BiV) database, a project launched by the Basque and Beyond (Bas&Be) research group. This open-access online database, available in both Basque and English versions, is intended to facilitate research on Basque morphosyntactic features that show cross-dialectal variation. Based on data obtained from questionnaires, the BiV provides the user with a description of each feature together with illustrative examples, and accompanies each entry with a map graphically depicting the distribution of variation. The resulting fine-grained picture of the distribution of morphosyntactic phenomena across Basque varieties has the ultimate goal of improving our understanding of the systematicities and connections that underlie variation. Thanks to its user-friendly format, the database can be used easily by anyone who is interested in Basque morphosyntax in particular and cross-linguistic variation in general. The results obtained thus far show that while some features have the same distribution across Basque varieties as that previously reported, others are spreading and thus have a wider geographical presence than has been described in the literature.

scholarly journals Covid19db – An online database of trials of medicinal products to prevent or treat COVID-19, with a specific focus on drug repurposing

2020 ◽  
Author(s):  
Pan Pantziarka ◽  
Liese Vandeborne ◽  
Lydie Meheus ◽  
Gauthier Bouche
Keyword(s):  
Clinical Trials ◽  
Open Access ◽  
Drug Repurposing ◽  
Online Database ◽  
Medicinal Products ◽  
Global Pandemic ◽  
Repurposed Drugs ◽  
Single Data ◽  
Clinical Trials Registry ◽  
User Friendly

AbstractBackgroundThe global pandemic caused by SARS-CoV-2 virus has prompted an unprecedented international effort to seek medicines for prevention and treatment of infection. Drug repurposing has played a key part in this response. The rapid increase in trial activity has raised questions about efficiency and lack of coordination. Our objective was to develop a user-friendly, open access, online database of interventional trials of medicinal products to monitor and rapidly identify trials of medicinal products.Methods and FindingsUsing the US clinicaltrials.gov (NCT) registry, the EU Clinical Trials Register (EUCTR) and the WHO International Clinical Trials Registry Platform (WHO ICTRP), we identified all COVID-19 trials of medicinal products and combined data from the 3 sources into a single data table. Trials that were out of scope and duplicates were excluded. A manual encoding was performed to ascertain key information (e.g. trial aim, type of intervention etc). The database, Covid19db, was published online at: http://www.redo-project.org/covid19db/. Descriptive statistics of the database from April 4th 2020 through to May 19th show an increase from 186 to 955 trials, or an average of 17 new trials registered per day. Over this period, the proportion of trials including a repurposing arm decreased slightly over time (from a maximum of 75% to 68% at the end of the covered period) as did the proportion of trials aiming to prevent infection (from a maximum of 16% to 12% at the end of the covered period). The most popular intervention is hydroxychloroquine (180 trials), followed by azithromycin (57 trials), chloroquine, tocilizumab and lopinavir/ritonavir (36 trials). Total planned enrolment is 468,559 participants as of 19th May 2020.Conclusionswe have developed an open access, online and regularly updated tool to monitor clinical trials of medicinal products to prevent or treat infection by SARS-CoV-2 globally. Our analysis shows a high number of ‘me-too’ trials, in particular for some repurposed drugs, such as hydroxychloroquine, azithromycin and tocilizumab, substantiating calls for better coordination and better use of trial resources.

MetaADEDB 2.0: a comprehensive database on adverse drug events

2020 ◽  
Author(s):  
Zhuohang Yu ◽  
Zengrui Wu ◽  
Weihua Li ◽  
Guixia Liu ◽  
Yun Tang
Keyword(s):  
Safety Assessment ◽  
Adverse Drug Events ◽  
Adverse Event Reporting System ◽  
Adverse Event Reporting ◽  
Supplementary Information ◽  
Online Database ◽  
Web Interface ◽  
Drug Discovery And Development ◽  
Comprehensive Information ◽  
User Friendly

Abstract Summary MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here, we reported its second version by collecting more and newer data from the U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Database, in addition to the original three sources. The new version consists of 744 709 drug–ADE associations between 8498 drugs and 13 193 ADEs, which has an over 40% increase in drug–ADE associations compared to the previous version. Meanwhile, we developed a new and user-friendly web interface for data search and analysis. We hope that MetaADEDB 2.0 could provide a useful tool for drug safety assessment and related studies in drug discovery and development. Availability and implementation The database is freely available at: http://lmmd.ecust.edu.cn/metaadedb/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals The Critical Role of Institutional Services in Open Access Advocacy

2013 ◽  
Vol 8 (1) ◽  
pp. 84-106 ◽  
Author(s):  
Tomasz Neugebauer ◽  
Annie Murray
Keyword(s):  
Open Access ◽  
Critical Role ◽  
Text Data ◽  
Relative Significance ◽  
Institutional Repositories ◽  
Time Commitment ◽  
Institutional Services ◽  
Service Oriented ◽  
User Friendly

This paper examines the development of the Open Access movement in scholarly communication, with particular attention to some of the rhetorical strategies and policy mechanisms used to promote it to scholars and scientists. Despite the majority of journal publishers’ acceptance of author self-archiving practices, and the minimal time commitment required by authors to successfully self-archive their work in disciplinary or institutional repositories, the majority of authors still by and large avoid participation. The paper reviews the strategies and arguments used for increasing author participation in open access, including the role of open access mandates. We recommend a service-oriented approach towards increasing participation in open access, rather than rhetoric that speculates on the benefits that open access will have on text/data mining innovation. In advocating for open access participation, we recommend focusing on its most universal and tangible purpose: increasing public open (gratis) access to the published results of publicly funded research. Researchers require strong institutional support to understand the copyright climate of open access self-archiving, user-friendly interfaces and useful metrics, such as repository usage statistics. We recommend that mandates and well-crafted and responsive author support services at universities will ultimately be required to ensure the growth of open access. We describe the mediated deposit service that was developed to support author self-archiving in Spectrum: Concordia University Research Repository. By comparing the number of deposits of non-thesis materials (e.g. articles and conference presentations) that were accomplished through the staff-mediated deposit service to the number of deposits that were author-initiated, we demonstrate the relative significance of this service to the growth of the repository.

scholarly journals Rapid advancement in cancer genomic big data in the pursuit of precision oncology

2021 ◽  
Author(s):  
Tiara Bunga Mayang Permata ◽  
Sri Mutya Sekarutami ◽  
Endang Nuryadi ◽  
Angela Giselvania ◽  
Soehartati Gondhowiardjo
Keyword(s):  
Big Data ◽  
Open Access ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Genomic Data ◽  
The Cancer Genome Atlas ◽  
Clinical Samples ◽  
Precision Oncology ◽  
Cancer Data ◽  
User Friendly

In the current big data era, massive genomic cancer data are available for open access from anywhere in the world. They are obtained from popular platforms, such as The Cancer Genome Atlas, which provides genetic information from clinical samples, and Cancer Cell Line Encyclopedia, which offers genomic data of cancer cell lines. For convenient analysis, user-friendly tools, such as the Tumor Immune Estimation Resource (TIMER), which can be used to analyze tumor-infiltrating immune cells comprehensively, are also emerging. In clinical practice, clinical sequencing has been recommended for patients with cancer in many countries. Despite its many challenges, it enables the application of precision medicine, especially in medical oncology. In this review, several efforts devoted to accomplishing precision oncology and applying big data for use in Indonesia are discussed. Utilizing open access genomic data in writing research articles is also described.

scholarly journals WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides

2019 ◽  
Vol 48 (D1) ◽  
pp. D389-D393 ◽  
Author(s):  
Nikolaos Louros ◽  
Katerina Konstantoulea ◽  
Matthias De Vleeschouwer ◽  
Meine Ramakers ◽  
Joost Schymkowitz ◽  
...  
Keyword(s):  
Open Access ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Structural Information ◽  
3D Models ◽  
Accurate Prediction ◽  
Binding Assays ◽  
Manual Curation ◽  
Open Access Database ◽  
User Friendly

Abstract Transition of soluble proteins into insoluble amyloid fibrils is driven by self-propagating short sequence stretches. However, accurate prediction of aggregation determinants remains challenging. Here, we describe WALTZ-DB 2.0, an updated and significantly expanded open-access database providing information on experimentally determined amyloid-forming hexapeptide sequences (http://waltzdb.switchlab.org/). We have updated WALTZ-DB 2.0 with new entries, including: (i) experimental validation of an in-house developed dataset of 229 hexapeptides, using electron microscopy and Thioflavin-T binding assays; (ii) manual curation of 98 amyloid-forming peptides isolated from literature. Furthermore, the content has been expanded by adding novel structural information for peptide entries, including sequences of the previous version. Using a computational methodology developed in the Switch lab, we have generated 3D-models of the putative amyloid fibril cores of WALTZ-DB 2.0 entries. Structural models, coupled with information on the energetic contributions and fibril core stabilities, can be accessed through individual peptide entries. Customized filtering options for subset selections and new modelling graphical features were added to upgrade online accessibility, providing a user-friendly interface for browsing, downloading and updating. WALTZ-DB 2.0 remains the largest open-access repository for amyloid fibril formation determinants and will continue to enhance the development of new approaches focused on accurate prediction of aggregation prone sequences.

scholarly journals Unity in Diversity?: A Fine-Grained Approach to Linguistic Geography of Breton by Means of Dialectometry

2019 ◽  
Vol 10 ◽  
pp. 137-174
Author(s):  
Tanguy Solliec ◽  
Keyword(s):  
Small Area ◽  
Local Variation ◽  
Computational Method ◽  
Linguistic Variation ◽  
Fine Grained ◽  
Unity In Diversity

Local variation in Breton is a well known feature but aggregate analyses on this topic are still rare. A dialectometric approach, i.e. a computational method for comparing data from the different locations of a linguistic atlas, applied to the Nouvel Atlas Linguistique de la Basse-Bretagne (Le Dû 2001) but restrained to a small area at the center of the Lower-Brittany has identified a few phenomena involved in linguistic variation and has quantified their importance. We discuss these results in the light of the frequency of these facts for each site. This approach is an opportunity to associate basic corpus approach to linguistic geography for a better understanding of linguistic variation.

scholarly journals Corpus-based Approaches to Constructional Change

2013 ◽  
Author(s):  
Martin Hilpert
Keyword(s):  
Quantitative Analysis ◽  
Corpus Linguistics ◽  
Linguistic Variation ◽  
Fine Grained

This chapter analyzes how corpus linguistics has significantly affected our understanding of constructional change. It describes three different kinds of constructional change, including changes in a construction's frequency, in its form, and in its function. The analysis reveals that, in all cases, the data retrieved from corpora can reveal fine-grained detail regarding the gradual nature of constructional change and facilitate the quantitative analysis that typifies much work on linguistic variation and change.

On the utility of combining production data and perceptual data to investigate regional linguistic variation: The case of Spanish experiential gustar ‘to like, to please’ on Twitter and in an online survey

2015 ◽  
Vol 3 (2) ◽  
pp. 47-59
Author(s):  
Earl K. Brown
Keyword(s):  
Social Networking ◽  
Online Survey ◽  
Descriptive Analysis ◽  
Linguistic Variation ◽  
Production Data ◽  
Mexican Spanish ◽  
Dialectal Variation ◽  
Syntactic Form ◽  
Spanish Speaking ◽  
The Social

The use of both production and perceptual data has the potential to provide a more complete picture of linguistic phenomena than would otherwise be the case, including when exploring regional linguistic variation. Utilizing the social networking platform Twitter and an online survey, this paper reports on a descriptive analysis of the geographic distribution of a less-commonly used syntactic form of the Spanish verbgustar‘to like, to please’, referred to as experientialgustar(e.g.,cuando gustes‘when you’d like’). The results from the analysis of 6,686 tweets together with the responses of 81 native Spanish-speaking participants in an online survey suggest that experientialgustaris produced and is perceived to be produced most often in Mexican Spanish, despite not being exclusive to that country. The paper contributes to the literature depicting the benefit of using both production and perceptual data in the study of dialectal variation, as well as to the literature documenting language variation in Spanish.

ISAPOnline as an enhancement of a service to community libraries making use of technological development

2002 ◽  
Vol 23 (2) ◽  
pp. 77-79
Author(s):  
Antoinette Kotze
Keyword(s):  
Technological Development ◽  
Information Service ◽  
Internet Access ◽  
Complete Information ◽  
Specific Reference ◽  
Online Database ◽  
Level Information ◽  
Multi Level ◽  
Community Libraries ◽  
User Friendly

The article highlights the features of the ISAP Online database with specific reference to community libraries: internet access, affordability, user-friendly searching, comprehensive and multi-level information content, and its role as a complete information service.

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