Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar
A peer-reviewed article of this Preprint also exists.
Author and article information
Abstract
The timely publication of scientific results is essential for dynamic advances in science. The ubiquitous availability of computers which are connected to a global network made the rapid and low-cost distribution of information through electronic channels possible. New concepts, such as Open Access publishing and preprint servers are currently changing the traditional print media business towards a community-driven peer production. However, the cost of scientific literature generation, which is either charged to readers, authors or sponsors, is still high. The main active participants in the authoring and evaluation of scientific manuscripts are volunteers, and the cost for online publishing infrastructure is close to negligible. A major time and cost factor is the formatting of manuscripts in the production stage. In this article we demonstrate the feasibility of writing scientific manuscripts in plain markdown (MD) text files, which can be easily converted into common publication formats, such as PDF, HTML or EPUB, using pandoc. The simple syntax of markdown assures the long-term readability of raw files and the development of software and workflows. We show the implementation of typical elements of scientific manuscripts – formulas, tables, code blocks and citations – and present tools for editing, collaborative writing and version control. We give an example on how to prepare a manuscript with distinct output formats, a DOCX file for submission to a journal, and a LATEX/PDF version for deposition as a PeerJ preprint. Further, we implemented new features for supporting ‘semantic web’ applications, such as the ‘journal article tag suite’ - JATS, and the ‘citation typing ontology’ - CiTO standard. Reducing the work spent on manuscript formatting translates directly to time and cost savings for writers, publishers, readers and sponsors. Therefore, the adoption of the MD format contributes to the agile production of open science literature. Pandoc Scholar is freely available from https://github.com/pandoc-scholar.
Cite this as
2017. Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. PeerJ Preprints 5:e2648v2 https://doi.org/10.7287/peerj.preprints.2648v2note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
The first version was improved according to reviewer's comments.
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Additional Information
Competing Interests
Albert Krewinkel is a voluntary member of the Pandoc Development Team. Robert Winkler is an Academic Editor for PeerJ. We have no financial/ legal conflict of interest.
Author Contributions
Albert Krewinkel conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper, programming.
Robert Winkler conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper, programming.
Data Deposition
The following information was supplied regarding data availability:
https://github.com/pandoc-scholar/pandoc-scholar
https://github.com/robert-winkler/scientific-articles-markdown/
Funding
The work was funded by the Consejo Nacional de Ciencia y Tecnología (CONACyT) Mexico, with the grant FRONTERAS 2015-2/814 and by institutional funding of the Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
