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Citation.js: a format-independent, modular bibliography tool for the browser and command line

Posted on by Hans Dillaerts

Author : Lars G Willighagen

Background

Given the vast number of standards and formats for bibliographical data, any program working with bibliographies and citations has to be able to interpret such data. This paper describes the development of Citation.js (https://citation.js.org/), a tool to parse and format according to those standards.

The program follows modern guidelines for software in general and JavaScript in specific, such as version control, source code analysis, integration testing and semantic versioning.

Results

The result is an extensible tool that has already seen adaption in a variety of sources and use cases: as part of a server-side page generator of a publishing platform, as part of a local extensible document generator, and as part of an in-browser converter of extracted references.

Use cases range from transforming a list of DOIs or Wikidata identifiers into a BibTeX file on the command line, to displaying RIS references on a webpage with added Altmetric badges to generating « How to cite this » sections on a blog.

The accuracy of conversions is currently 27 % for properties and 60 % for types on average and a typical initialization takes 120 ms in browsers and 1 s with Node.js on the command line.

Conclusions

Citation.js is a library supporting various formats of bibliographic information in a broad selection of use cases and environments. Given the support for plugins, more formats can be added with relative ease.

URL : Citation.js: a format-independent, modular bibliography tool for the browser and command line

DOI : https://doi.org/10.7287/peerj.preprints.27466v2

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Open collaborative writing with Manubot

Posted on by Hans Dillaerts

Authors : Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

Open, collaborative research is a powerful paradigm that can immensely strengthen the scientific process by integrating broad and diverse expertise. However, traditional research and multi-author writing processes break down at scale.

We present new software named Manubot, available at https://manubot.org, to address the challenges of open scholarly writing. Manubot adopts the contribution workflow used by many large-scale open source software projects to enable collaborative authoring of scholarly manuscripts.

With Manubot, manuscripts are written in Markdown and stored in a Git repository to precisely track changes over time. By hosting manuscript repositories publicly, such as on GitHub, multiple authors can simultaneously propose and review changes.

A cloud service automatically evaluates proposed changes to catch errors. Publication with Manubot is continuous: When a manuscript’s source changes, the rendered outputs are rebuilt and republished to a web page.

Manubot automates bibliographic tasks by implementing citation by identifier, where users cite persistent identifiers (e.g. DOIs, PubMed IDs, ISBNs, URLs), whose metadata is then retrieved and converted to a user-specified style.

Manubot modernizes publishing to align with the ideals of open science by making it transparent, reproducible, immediate, versioned, collaborative, and free of charge.

URL : Open collaborative writing with Manubot

DOI : https://doi.org/10.1371/journal.pcbi.1007128

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Share or perish: Social media and the International Journal of Mental Health Nursing

Posted on by Hans Dillaerts

Authors : Paul McNamara, Kim Usher

The impact of published research is sometimes measured by the number of citations an individual article accumulates. However, the time from publication to citation can be extensive. Years may pass before authors are able to measure the impact of their publication. Social media provides individuals and organizations a powerful medium with which to share information.

The power of social media is sometimes harnessed to share scholarly works, especially journal article citations and quotes. A non‐traditional bibliometric is required to understand the impact social media has on disseminating scholarly works/research.

The International Journal of Mental Health Nursing (IJMHN) appointed a social media editor as of 1 January 2017 to implement a strategy to increase the impact and reach of the journal’s articles.

To measure the impact of the IJMHN social media strategy, quantitative data for the eighteen months prior to the social media editor start date, and the eighteen months after that date (i.e.: from 01 July 2015 to 30 June 2018) were acquired and analysed.

Quantitative evidence demonstrates the effectiveness of one journal’s social media strategy in increasing the reach and readership of the articles it publishes.

This information may be of interest to those considering where to publish their research, those wanting to amplify the reach of their research, those who fund research, and journal editors and boards.

DOI : https://doi.org/10.1111/inm.12600

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Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives

Posted on by Hans Dillaerts

Authors : Charles Vesteghem, Rasmus Froberg Brøndum, Mads Sønderkær, Mia Sommer, Alexander Schmitz, Julie Støve Bødker, Karen Dybkær, Tarec Christoffer El-Galaly, Martin Bøgsted

Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance.

The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives.

For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively.

For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society’s standard.

For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.

URL : Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives

DOI : https://doi.org/10.1093/bib/bbz044

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The complex nature of research dissemination practices among public health faculty researchers

Posted on by Hans Dillaerts

Authors : Rosie Hanneke, Jeanne M. Link

Objective

This study explores the variety of information formats used and audiences targeted by public health faculty in the process of disseminating research.

Methods

The authors conducted semi-structured interviews with twelve faculty members in the School of Public Health at the University of Illinois at Chicago, asking them about their research practices, habits, and preferences.

Results

Faculty scholars disseminate their research findings in a variety of formats intended for multiple audiences, including not only their peers in academia, but also public health practitioners, policymakers, government and other agencies, and community partners.

Conclusion

Librarians who serve public health faculty should bear in mind the diversity of faculty’s information needs when designing and improving library services and resources, particularly those related to research dissemination and knowledge translation.

Promising areas for growth in health sciences libraries include supporting data visualization, measuring the impact of non-scholarly publications, and promoting institutional repositories for dissemination of research.

URL : The complex nature of research dissemination practices among public health faculty researchers

Alternative location : http://jmla.pitt.edu/ojs/jmla/article/view/524

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The impact of digital copyright law and policy on access to knowledge and learning

Posted on by Hans Dillaerts

Authors : Tana Pistorius, Odirachukwu S. Mwim

Background

The evolution in digital technologies has had an enormous impact on traditional copyright notions. Works in digital form have uniform characteristics and these works can be copied, distributed and stored with ease.

Objectives

The focus of this article was how to attain a balance between the need to promote access to works and therefore knowledge and learning, on the one hand, and the protection of the interests of copyright holders, on the other.

Method

Technological protection measures (TPMs) are applied to copyright works in digital form to curb infringement. The authors explore the extent to which TPMs impact on access the knowledge and learning.

Results

The findings of this article suggest a need for possible countermeasures in promoting knowledge and literacy through legislative reform that address the needs of creators and users in developing communities.

Conclusion

The authors conclude that TPMs may hinder data literacy, access to works, teaching and learning, particularly in developing communities. For example, recent attempts to revise South African copyright law have not attained a balanced approach.

URL : The impact of digital copyright law and policy on access to knowledge and learning

DOI : https://doi.org/10.4102/rw.v10i1.196

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The citation advantage of linking publications to research data

Posted on by Hans Dillaerts

Authors : Giovanni Colavizza, Iain Hrynaszkiewicz, Isla Staden, Kirstie Whitaker, Barbara McGillivray

Efforts to make research results open and reproducible are increasingly reflected by journal policies encouraging or mandating authors to provide data availability statements.

As a consequence of this, there has been a strong uptake of data availability statements in recent literature. Nevertheless, it is still unclear what proportion of these statements actually contain well-formed links to data, for example via a URL or permanent identifier, and if there is an added value in providing them.

We consider 531,889 journal articles published by PLOS and BMC which are part of the PubMed Open Access collection, categorize their data availability statements according to their content and analyze the citation advantage of different statement categories via regression.

We find that, following mandated publisher policies, data availability statements have become common by now, yet statements containing a link to a repository are still just a fraction of the total.

We also find that articles with these statements, in particular, can have up to 25.36% higher citation impact on average: an encouraging result for all publishers and authors who make the effort of sharing their data. All our data and code are made available in order to reproduce and extend our results.

URL : https://arxiv.org/abs/1907.02565