Submitted 19 December 2016
Accepted 3 April 2017
Published 8 May 2017
Corresponding author
Robert Winkler,
robert.winkler@cinvestav.mx
Academic editor
Sebastian Ventura
Additional Information and
Declarations can be found on
page 20
DOI 10.7717/peerj-cs.112
Copyright
2017 Krewinkel and Winkler
Distributed under
Creative Commons CC-BY 4.0
OPEN ACCESS
Formatting Open Science: agilely creating
multiple document formats for academic
manuscripts with Pandoc Scholar
Albert Krewinkel1 and Robert Winkler2
1 Pandoc Development Team, Berlin, Germany
2 Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Mexico
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.
Subjects Human–Computer Interaction, Computer Education, Computer Networks and
Communications, Digital Libraries, World Wide Web and Web Science
Keywords Open science, Markdown, Latex, Publishing, Typesetting, Document formats
INTRODUCTION
Agile development of science depends on the continuous exchange of information between
researchers (Woelfle, Olliaro & Todd, 2011). In the past, physical copies of scientific works
had to be produced and distributed. Therefore, publishers needed to invest considerable
How to cite this article Krewinkel and Winkler (2017), Formatting Open Science: agilely creating multiple document formats for aca-
demic manuscripts with Pandoc Scholar. PeerJ Comput. Sci. 3:e112; DOI 10.7717/peerj-cs.112
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https://peerj.com/academic-boards/editors/
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resources for typesetting and printing. Since the journals were mainly financed by their
subscribers, their editors not only had to decide on the scientific quality of a submitted
manuscript, but also on the potential interest to their readers. The availability of globally
connected computers enabled the rapid exchange of information at low cost. Yochai
Benkler (2006) predicts important changes in the information production economy, which
are based on three observations:
1. A nonmarket motivation in areas such as education, arts, science, politics and theology.
2. The actual rise of nonmarket production, made possible through networked individuals
and coordinate effects.
3. The emergence of large-scale peer production; for example, of software and
encyclopedias.
Immaterial goods such as knowledge and culture are not lost when consumed or
shared—they are ‘nonrival’—, and they enable a networked information economy, which
is not commercially driven (Benkler, 2006).
Preprints and e-prints
In some areas of science a preprint culture, i.e., a paper-based exchange system of research
ideas and results, already existed when Paul Ginsparg in 1991 initiated a server for the
distribution of electronic preprints—‘e-prints’—about high-energy particle theory at the
Los Alamos National Laboratory (LANL), USA (Ginsparg, 1994). Later, the LANL server
moved with Ginsparg to Cornell University, USA, and was renamed as arXiv (Butler, 2001).
Currently, arXiv (https://arxiv.org/) publishes e-prints related to physics, mathematics,
computer science, quantitative biology, quantitative finance and statistics. Just a few
years after the start of the first preprint servers, their important contribution to scientific
communication was evident (Ginsparg, 1994; Youngen, 1998; Brown, 2001). In 2014, arXiv
reached the impressive number of 1 million e-prints (Van Noorden, 2014).
In more conservative areas, such as chemistry and biology, accepting the publishing
prior peer-review took more time (Brown, 2003). A preprint server for life sciences
(http://biorxiv.org/) was launched by the Cold Spring Habor Laboratory, USA, in
2013 (Callaway, 2013). PeerJ preprints (https://peerj.com/preprints/), started in the same
year, accepts manuscripts from biological sciences, medical sciences, health sciences and
computer sciences.
The terms ‘preprints’ and ‘e-prints’ are used synonymously, since the physical
distribution of preprints has become obsolete. A major drawback of preprint publishing are
the sometimes restrictive policies of scientific publishers. The SHERPA/RoMEO project
informs about copyright policies and self-archiving options of individual publishers
(http://www.sherpa.ac.uk/romeo/).
Open Access
The term ‘Open Access’ (OA) was introduced 2002 by the Budapest Open Access Initiative
and was defined as:
‘‘Barrier-free access to online works and other resources. OA literature is digital, online,
free of charge (gratis OA), and free of needless copyright and licensing restrictions (libre OA).’’
(Suber, 2012)
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https://arxiv.org/
http://biorxiv.org/
https://peerj.com/preprints/
http://www.sherpa.ac.uk/romeo/
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Frustrated by the difficulty to access even digitized scientific literature, three scientists
founded the Public Library of Science (PLoS). In 2003, PLoS Biology was published as the
first fully Open Access journal for biology (Brown, Eisen & Varmus, 2003; Eisen, 2003).
Thanks to the great success of OA publishing, many conventional print publishers now
offer a so-called ‘Open Access option’, i.e., to make accepted articles free to read for an addi-
tional payment by the authors. The copyright in these hybrid models might remain with the
publisher, whilst fully OA usually provide a liberal license, such as the Creative Commons
Attribution 4.0 International (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/).
OA literature is only one component of a more general open philosophy, which also
includes the access to scholarships, software, and data (Willinsky, 2005). Interestingly, there
are several different ‘schools of thought’ on how to understand and define Open Science,
as well the position that any science is open by definition, because of its objective to make
generated knowledge public (Fecher & Friesike, 2014).
Cost of journal article production
In a recent study, the article processing charges (APCs) for research intensive universities
in the USA and Canada were estimated to be about 1,800 USD for fully OA journals and
3,000 USD for hybrid OA journals (Solomon & Björk, 2016). PeerJ (https://peerj.com/), an
OA journal for biological and computer sciences launched in 2013, drastically reduced the
publishing cost, offering its members a life-time publishing plan for a small registration fee
(Van Noorden, 2012); alternatively the authors can choose to pay an APC of $1,095 USD,
which may be cheaper, if multiple co-authors participate.
Examples such as the Journal of Statistical Software (JSS, https://www.jstatsoft.org/) and
eLife (https://elifesciences.org/) demonstrate the possibility of completely community-
supported OA publications. Figure 1 compares the APCs of different OA publishing
business models.
JSS and eLife are peer-reviewed and indexed by Thomson Reuters. Both journals are
located in the Q1 quality quartile in all their registered subject categories of the Scimago
Journal & Country Rank (http://www.scimagojr.com/), demonstrating that high-quality
publications can be produced without charging the scientific authors or readers.
In 2009, a study was carried out concerning the ‘‘Economic Implications of Alternative
Scholarly Publishing Models’’, which demonstrates an overall societal benefit by using OA
publishing models (Houghton et al., 2009). In the same report, the real publication costs
are evaluated. The relative costs of an article for the publisher are presented in Fig. 2.
Conventional publishers justify their high subscription or APC prices with the added
value; for example, journalism (stated in the graphics as ‘non-article processing’). However,
stakeholder profits, which could be as high as 50%, also must be considered, and are
withdrawn from the science budget (Van Noorden, 2013).
Generally, the production costs of an article could be roughly divided into commercial
and academic/technical costs (Fig. 2). For nonmarket production, the commercial costs
such as margins/profits, management etc. can be drastically reduced. Hardware and services
for hosting an editorial system, such as Open Journal Systems of the Public Knowledge
Project (https://pkp.sfu.ca/ojs/) can be provided by public institutions. Employed scholars
Krewinkel and Winkler (2017), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.112 3/23
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https://creativecommons.org/licenses/by/4.0/
https://peerj.com/
https://www.jstatsoft.org/
https://elifesciences.org/
http://www.scimagojr.com/
https://pkp.sfu.ca/ojs/
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Figure 1 Article Processing Charge (APCs) that authors have to pay for with different Open Access
(OA) publishing models. Data from Solomon & Björk (2016) and journal web-pages.
Figure 2 Estimated publishing cost for a ‘hybrid’ journal (conventional with Open Access option).
Data from Houghton et al. (2009).
can perform editor and reviewer activities without additional cost for the journals.
Nevertheless, ‘article processing’, which includes the manuscript handling during peer
review and production represents the most expensive part.
Therefore, we investigated a strategy for the efficient formatting of scientific manuscripts.
Current standard publishing formats
Generally speaking, a scientific manuscript is composed of contents and formatting. While
the content, i.e., text, figures, tables, citations etc., may remain the same between different
publishing forms and journal styles, the formatting can be very different. Most publishers
require the formatting of submitted manuscripts in a certain format. Ignoring this Guide
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Table 1 Current standard formats for scientific publishing.
Type Description Use Syntax Reference
DOCX Office Open XML WYSIWYG editing XML, ZIP Ngo (2006)
ODT OpenDocument WYSIWYG editing XML, ZIP Brauer et al. (2005)
PDF Portable document Print replacement PDF International Organization for Standardizationd (2013)
EPUB Electronic publishing e-books HTML5, ZIP Eikebrokk, Dahl & Kessel (2014)
JATS Journal article tag suite Journal publishing XML National Information Standards Organization (2012)
LATEX Typesetting system High-quality print TEX Lamport (1994)
HTML Hypertext markup Websites (X)HTML Raggett, Le Hors & Jacobs (1999) and Hickson et al. (2014)
MD Markdown Lightweight markup Plain text MD Ovadia (2014) and Leonard (2016)
Table 2 Examples for formatting elements and their implementations in different markup languages.
Element Markdown LATEX HTML
Structure
Section # Intro \section{Intro} Intro
Subsection ## History \subsection{History} History
Text style
Bold **text** \textbf{text} text
Italics *text* \textit{text} text
Links
HTTP link \usepackage{url}\url{https://arxiv.org}
for Authors, (for example, by submitting a manuscript with a different reference style),
gives a negative impression with a journal’s editorial staff. Manuscripts which are too
carelessly prepared can even provoke a straight ‘desk-reject’ (Volmer & Stokes, 2016).
Currently DOC(X), LATEX and/ or PDF file formats are the most frequently used
formats for journal submission platforms. However, even if the content of a submitted
manuscript might be accepted during the peer review ‘as is’, the format still needs to
be adjusted to the particular publication style in the production stage. For the electronic
distribution and archiving of scientific works, which is gaining more and more importance,
additional formats (EPUB, (X)HTML, JATS) need to be generated. Table 1 lists the file
formats which are currently the most relevant ones for scientific publishing.
Although the content elements of documents, such as title, author, abstract, text,
figures, tables, etc., remain the same, the syntax of the file formats is rather different.
Table 2 demonstrates some simple examples of differences in different markup languages.
Documents with the commonly used Office Open XML (DOCX Microsoft Word files)
and OpenDocument (ODT LibreOffice) file formats can be opened in a standard text
editor after unzipping. However, content and formatting information is distributed into
various folders and files. Practically speaking, those file formats require the use of special
word processing software.
From a writer’s perspective, the use of What You See Is What You Get (WYSIWYG)
programs such as Microsoft Word, WPS Office or LibreOffice might be convenient, because
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the formatting of the document is directly visible. But the complicated syntax specifications
often result in problems when using different software versions and for collaborative
writing. Simple conversions between file formats can be difficult or impossible. In a
worst-case scenario, ‘old’ files cannot be opened any more for lack of compatible software.
In some parts of the scientific community therefore LATEX, a typesetting program
in plain text format, is very popular. With LATEX, documents with highest typographic
quality can be produced. However, the source files are cluttered with LATEX commands
and the source text can be complicated to read. Causes of compilation errors in LATEX
are sometimes difficult to find. Therefore, LATEX is not very user friendly, especially for
casual writers or beginners.
In academic publishing, it is additionally desirable to create different output formats
from the same source text:
• For the publishing of a book, with a print version in PDF and an electronic version in
EPUB.
• For the distribution of a seminar script, with an online version in HTML and a print
version in PDF.
• For submitting a journal manuscript for peer-review in DOCX, as well as a preprint
version with another journal style in PDF.
• For archiving and exchanging article data using the Journal Article Tag Suite (JATS)
(National Information Standards Organization, 2012), a standardized format developed
by the National Library of Medicine (NLM).
Some of the tasks can be performed with LATEX, but an integrated solution remains
a challenge. Several programs for the conversion between documents formats exist, such
as the e-book library program calibre (http://calibre-ebook.com/). But the results of such
conversions are often not satisfactory and require substantial manual corrections.
Therefore, we were looking for a solution that enables the creation of scientific
manuscripts in a simple format, with the subsequent generation of multiple output
formats. The need for hybrid publishing has been recognized outside of science (Kielhorn,
2011), but the requirements specific to scientific publishing have not been addressed so far.
Therefore, we investigated the possibility to generate multiple publication formats from a
simple manuscript source file.
CONCEPTS OF MARKDOWN AND PANDOC
Markdown was originally developed by John Gruber in collaboration with Aaron Swartz,
with the goal to simplify the writing of HTML documents (http://daringfireball.net/
projects/markdown/). Instead of coding a file in HTML syntax, the content of a document
is written in plain text and annotated with simple tags which define the formatting.
Subsequently, the Markdown (MD) files are parsed to generate the final HTML document.
With this concept, the source file remains easily readable and the author can focus on the
contents rather than formatting. Despite its original focus on the web, the MD format
has been proven to be well suited for academic writing (Ovadia, 2014). In particular,
Pandoc-flavored MD (http://pandoc.org/) adds several extensions which facilitate the
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http://calibre-ebook.com/
http://daringfireball.net/projects/markdown/
http://daringfireball.net/projects/markdown/
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Figure 3 Workfow for the generation of multiple document formats with Pandoc. The markdown
(MD) file contains the manuscript text with formatting tags, and can also refer to external files such as
images or reference databases. The Pandoc processor converts the MD file to the desired output formats.
Documents, citations etc. can be defined in style files or templates.
authoring of academic documents and their conversion into multiple output formats.
Table 2 demonstrates the simplicity of MD compared to other markup languages. Figure 3
illustrates the generation of various formatted documents from a manuscript in Pandoc
MD. Some relevant functions for scientific texts are explained below in more detail.
MARKDOWN EDITORS AND ONLINE EDITING
The usability of a text editor is important for the author, either writing alone or with
several co-authors. In this section we present software and strategies for different scenarios.
Figure 4 summarizes various options for local or networked editing of MD files.
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Figure 4 Markdown files can be edited on local devices or on cloud drives. A local or remote Git reposi-
tory enables advanced advanced version control.
Markdown editors
Due to MD’s simple syntax, basically any text editor is suitable for editing markdown
files. The formatting tags are written in plain text and are easy to remember.
Therefore, the author is not distracted by looking around for layout options with
the mouse. For several popular text editors, such as vim (http://www.vim.org/),
GNU Emacs (https://www.gnu.org/software/emacs/), atom (https://atom.io/) or geany
(http://www.geany.org/), plugins provide additional functionality for markdown editing;
for example, syntax highlighting, command helpers, live preview or structure browsing.
Various dedicated markdown editors have been published as well. Many of those are
cross-platform compatible, such as Abricotine (http://abricotine.brrd.fr/), ghostwriter
(https://github.com/wereturtle/ghostwriter) and CuteMarkEd (https://cloose.github.io/
CuteMarkEd/).
The lightweight format is also ideal for writing on mobile devices. Numerous applications
are available on the App stores for Android and iOS systems. The programs Swype and
Dragon (http://www.nuance.com/) facilitate the input of text on such devices by guessing
words from gestures and speech recognition (dictation).
Figure 5 shows the editing of a markdown file, using the cross-platform editor Atom
with several markdown plugins.
Online editing and collaborative writing
Storing manuscripts on network drives (The Cloud) has become popular for several reasons:
• Protection against data loss.
• Synchronization of documents between several devices.
• Collaborative editing options.
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http://www.vim.org/
https://www.gnu.org/software/emacs/
https://atom.io/
http://www.geany.org/
http://abricotine.brrd.fr/
https://github.com/wereturtle/ghostwriter
https://cloose.github.io/CuteMarkEd/
https://cloose.github.io/CuteMarkEd/
http://www.nuance.com/
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Figure 5 Document directory tree, editing window and HTML preview using the Atom editor.
Markdown files on a Google Drive (https://drive.google.com) for instance can be edited
online with StackEdit (https://stackedit.io). Figure 6 demonstrates the online editing of
a markdown file on an ownCloud (https://owncloud.com/) installation. OwnCloud is an
Open Source software platform, which allows the set-up of a file server on personal web-
space. The functionality of an ownCloud installation can be enhanced by installing plugins.
Even mathematical formulas are rendered correctly in the HTML live preview window
of the ownCloud markdown plugin (Fig. 6).
The collaboration and authoring platform Authorea (https://www.authorea.com/) also
supports markdown as one of multiple possible input formats. This can be beneficial for
collaborations in which one or more authors are not familiar with markdown syntax.
Document versioning and change control
Programmers, especially when working in distributed teams, rely on version control
systems to manage changes of code. Currently, Git (https://git-scm.com/), which is also
used for the development of the Linux kernel, is one of the most employed software
solutions for versioning. Git allows the parallel work of collaborators and has an efficient
merging and conflict resolution system. A Git repository may be used by a single local
author to keep track of changes, or by a team with a remote repository; for example, on
Github (https://github.com/) or Bitbucket (https://bitbucket.org/). Because of the plain
text format of markdown, Git can be used for version control and distributed writing. For
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https://drive.google.com
https://stackedit.io
https://owncloud.com/
https://www.authorea.com/
https://git-scm.com/
https://github.com/
https://bitbucket.org/
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Figure 6 Direct online editing of this manuscript with live preview using the ownCloud Markdown Editor plugin by Robin Appelman.
the writing of the present article, the co-authors (Germany and Mexico) used a remote Git
repository on Bitbucket. The plain text syntax of markdown facilitates the visualization of
differences of document versions, as shown in Fig. 7.
PANDOC MARKDOWN FOR SCIENTIFIC TEXTS
In the following section, we demonstrate the potential for typesetting scientific manuscripts
with Pandoc using examples for typical document elements, such as tables, figures,
formulas, code listings and references. A brief introduction is given by Dominici (2014).
The complete Pandoc User’s Manual is available at http://pandoc.org/MANUAL.html.
Tables
There are several options to write tables in markdown. The most flexible alternative—which
was also used for this article—are pipe tables. The contents of different cells are separated
by pipe symbols (|):
Left | Center | Right | Default
:-----|:------:|------:|---------
LLL | CCC | RRR | DDD
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Figure 7 Version control and collaborative editing using a Git repository on Bitbucket.
gives
Left Center Right Default
LLL CCC RRR DDD
The headings and the alignment of the cells are given in the first two lines. The cell width
is variable. The Pandoc parameter --columns=NUM can be used to define the length of lines
in characters. If contents do not fit, they will be wrapped.
Complex tables (for example, tables featuring multiple headers or those containing cells
spanning multiple rows or columns), are currently not representable in Markdown format.
However, it is possible to embed LATEX and HTML tables into the document. These
format-specific tables will only be included in the output if a document of the respective
format is produced. This is method can be extended to apply any kind of format-specific
typographic functionality which would otherwise be unavailable in Markdown syntax.
Figures and images
Images are inserted as follows:
e.g.,
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The alt text is used e.g., in HTML output. Image dimensions can be defined in braces:
{width=50mm}
As well, an identifier for the figure can be defined with #, resulting e.g., in the image
attributes {#figure1 height=30%}.
A paragraph containing only an image is interpreted as a figure. The alt text is then
output as the figure’s caption.
Symbols
Scientific texts often require special characters; for example, Greek letters, mathematical
and physical symbols, and so on.
The UTF-8 standard, developed and maintained by the Unicode Consortium, enables
the use of characters across languages and computer platforms. The encoding is defined
as RFC document 3629 of the Network Working group (Yergeau, 2003) and as ISO
standard ISO/IEC 10646:2014 (International Organization for Standardization, 2014).
Specifications of Unicode and code charts are provided on the Unicode homepage
(http://www.unicode.org/).
In Pandoc Markdown documents, Unicode characters such as ◦, α, ä, Å can
be inserted directly and passed to the different output documents. The correct
processing of MD with UTF-8 encoding to LATEX/PDF output requires the use of the
--latex-engine=xelatex option and the use of an appropriate font. The Times-like XITS
font (https://github.com/khaledhosny/xits-math), suitable for high quality typesetting of
scientific texts, can be set in the LATEX template:
\usepackage{unicode-math}
\setmainfont
[ Extension = .otf,
UprightFont = *-regular,
BoldFont = *-bold,
ItalicFont = *-italic,
BoldItalicFont = *-bolditalic,
]{xits}
\setmathfont
[ Extension = .otf,
BoldFont = *bold,
]{xits-math}
To facilitate the input of specific characters, so-called mnemonics can be enabled
in some editors (e.g., in atom by the character-table package). For example, the 2-
character mnemonics ‘:u’ gives ‘ü’ (diaeresis), or ‘D*’ the Greek 1. The possible character
mnemonics and character setsare listed in RFC 1345: http://www.faqs.org/rfcs/rfc1345.html
(Simonsen, 1992).
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Formulas
Formulas are written in LATEX mode using the delimiters $. For example, the formula for
calculating the standard deviation s of a random sampling would be written as:
$s=\sqrt{\frac{1}{N-1}\sum_{i=1}^N(x_i-\overline{x})^{2}}$
and gives:
s=
√√√√ 1
N −1
N∑
i=1
(xi−x)2
with xi the individual observations, x the sample mean and N the total number of samples.
Pandoc parses formulas into internal structures and allows conversion into formats
other than LATEX. This allows for format-specific formula representation and enables
computational analysis of the formulas (Corbí& Burgos, 2015).
Code listings
Verbatim code blocks are indicated by three tilde symbols:
~~~
verbatim code
~~~
Typesetting inline code is possible by enclosing text between back ticks.
‘inline code‘
Other document elements
These examples are only a short demonstration of the capacities of Pandoc concerning
scientific documents. For more detailed information, we refer to the official manual
(http://pandoc.org/MANUAL.html).
CITATIONS AND BIOGRAPHY
The efficient organization and typesetting of citations and bibliographies is crucial
for academic writing. Pandoc supports various strategies for managing references. For
processing the citations and the creation of the bibliography, the command line parameter
--filter pandoc-citeproc is used, with variables for the reference database and
the bibliography style. The bibliography will be located automatically at the header
# References or # Bibliography.
Reference databases
Pandoc is able to process all mainstream literature database formats, such as RIS, BIB, etc.
However, for maintaining compatibility with LATEX/ BIBTEX, the use of BIB databases
is recommended. The used database either can be defined in the YAML metablock of the
MD file (see below) or it can be passed as parameter when calling Pandoc.
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Inserting citations
For inserting a reference, the database key is given within square brackets, and indicated
by an ‘@’. It is also possible to add information, such as page:
[@suber_open_2012; @benkler_wealth_2006, 57 ff.]
gives (Suber, 2012; Benkler, 2006, p. 57 ff.).
Styles
The Citation Style Language (CSL) (http://citationstyles.org/) is used for the citations and
bibliographies. This file format is supported, for example, by the reference management
programs Mendeley (https://www.mendeley.com/), Papers (http://papersapp.com/) and
Zotero (https://www.zotero.org/). CSL styles for particular journals can be found from
the Zotero style repository (https://www.zotero.org/styles). The bibliography style that
Pandoc should use for the target document can be chosen in the YAML block of the
Markdown document or can be passed in as an command line option. The latter is more
recommendable, because distinct bibliography style may be used for different documents.
Creation of LATEX natbib citations
For citations in scientific manuscripts written in LATEX, the natbib package is widely used.
To create a LATEX output file with natbib citations, Pandoc simply has to be run with the
--natbib option, but without the --filter pandoc-citeproc parameter.
Database of cited references
To share the bibliography for a certain manuscript with co-authors or the publisher’s
production team, it is often desirable to generate a subset of a larger database,
which only contains the cited references. If LATEX output was generated with the
--natbib option, the compilation of the file with LATEX gives an AUX file (in the
example named md-article.aux), which subsequently can be extracted using BibTool
(https://github.com/ge-ne/bibtool):
~~~
bibtool -x md-article.aux -o bibshort.bib
~~~
In this example, the article database will be called bibshort.bib.
For the direct creation of an article specific BIB database without using LATEX, we wrote
a simple Perl script called mdbibexport (https://github.com/robert-winkler/mdbibexport).
META INFORMATION OF THE DOCUMENT
Bourne (2005) argues that journals should be effectively equivalent to biological databases:
both provide data which can be referenced by unique identifiers like DOI or, for example,
gene IDs. Applying the semantic-web ideas of Berners-Lee & Hendler (2001) to this domain
can make this vision a reality. Here we show how metadata can be specified in Markdown.
We propose conventions, and demonstrate their suitability to enable interlinked and
semantically enriched journal articles.
Krewinkel and Winkler (2017), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.112 14/23
https://peerj.com
http://citationstyles.org/
https://www.mendeley.com/
http://papersapp.com/
https://www.zotero.org/
https://www.zotero.org/styles
https://github.com/ge-ne/bibtool
https://github.com/robert-winkler/mdbibexport
http://dx.doi.org/10.7717/peerj-cs.112
Document information such as title, authors, abstract etc. can be defined in a metadata
block written in YAML syntax. YAML (‘‘YAML Ain’t Markup Language’’, http://yaml.org/)
is a data serialization standard in simple, human readable format. Variables defined in the
YAML section are processed by Pandoc and integrated into the generated documents. The
YAML metadata block is recognized by three hyphens (---) at the beginning, and three
hyphens or dots (...) at the end; for example;
---
title: Formatting Open Science
subtitle: agile creation of multiple document types
date: 2017-02-10
...
The public availability of all relevant information is a central aspect of Open Science.
Analogous to article contents, data should be accessible via default tools. We believe that
this principle must also be applied to article metadata. Thus, we created a custom Pandoc
writer that emits the article’s data as JSON–LD (Lanthaler & Gütl, 2012), allowing for
informational and navigational queries of the journal’s data with standard tools of the
semantic web. The above YAML information would be output as:
{
"@context": {
"@vocab": "http://schema.org/",
"date": "datePublished",
"title": "headline",
"subtitle": "alternativeTitle"
},
"@type": "ScholarlyArticle",
"title": "Formatting Open Science",
"subtitle": "agile creation of multiple document types",
"date": "2017-02-10"
}
This format allows processing of the information by standard data processing software
and browsers.
Flexible metadata authoring
We developed a method to allow writers the flexible specification of authors and their
respective affiliations. Author names can be given as a string, via the key of a single-element
object, or explicitly as a name attribute of an object. Affiliations can be specified directly as
properties of the author object, or separately in the institute object.
Additional information, for example, email addresses or identifiers like ORCID (Haak
et al., 2012), can be added as additional values:
author:
- John Doe:
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http://yaml.org/
http://dx.doi.org/10.7717/peerj-cs.112
institute: fs
email: john.doe@example.com
orcid: 0000-0000-0000-0000
institute:
fs: Science Formatting Working Group
JATS support
The journal article tag suite (JATS) was developed by the National Library of Medicine
(NLM) and standardized by ANSI/NISO as an archiving and exchange format of journal
articles and the associated metadata (National Information Standards Organization, 2012),
including data of the type shown above. The pandoc-jats writer by Martin Fenner is a
plugin usable with Pandoc to produce JATS-formatted output. The writer was adapted to
be compatible with our metadata authoring method, allowing for simple generation of files
which contain the relevant metadata.
Citation types
Writers can add information about the reason a citation is given. This might help
reviewers and readers, and can simplify the search for relevant literature. We developed
an extended citation syntax that integrates seamlessly into Markdown and can be used to
add complementary information to citations. Our method is based on CiTO, the Citation
Typing Ontology (Shotton, 2010), which specifies a vocabulary for the motivation when
citing a resource. The type of a citations can be added to a Markdown citation using
@CITO_PROPERTY:KEY, where CITO_PROPERTY is a supported CiTO property, and KEY is
the usual citation key. Our tool extracts that information and includes it in the generated
linked data output. A general CiTO property (cites) is used, if no CiTO property is found
in a citation key.
The work at hand will always be the subject of the generated semantic subject–predicate–
object triples. Some CiTO predicates cannot be used in a sensical way under this condition.
Focusing on author convenience, we use this fact to allow shortening of properties when
sensible. For example, if authors of a biological paper include a reference to the paper
describing a method which was used in their work, this relation can be described by the
uses_method_in property of the CiTO ontology. The inverse property, provides_method_for,
would always be nonsensical in this context as implied by causality. It is therefore not
supported by our tool. This allows us to introduce an abbreviation (method) for the latter
property, as any ambiguity has been eliminated. Users of Western blotting might hence
write @method_in:towbin_1979 or even just @method:towbin_1979, where towbin_1979
is the citation identifier of the describing paper by Towbin, Staehelin & Gordon (1979).
EXAMPLE: MANUSCRIPT WITH OUTPUT OF DOCX/ODT
FORMAT AND LATEX/PDF FOR SUBMISSION TO
DIFFERENT JOURNALS
Scientific manuscripts have to be submitted in a format defined by the journal or publisher.
At the moment, DOCX is the most common file format for manuscript submission. Some
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http://dx.doi.org/10.7717/peerj-cs.112
publishers also accept or require LATEX or ODT formats. Additional to the general style of
the manuscript—organization of sections, fonts, etc.—the citation style of the journal must
also be followed. Often, the same manuscript has to be prepared for different journals;
for example, if the manuscript was rejected by a journal and has to be formatted for
another one, or if a preprint of the paper is submitted to an archive that requires a distinct
document format than the targeted peer-reviewed journal. In this example, we want to
create a manuscript for a PLoS journal in DOCX and ODT format for WYSIWYG word
processors. Further, a version in LATEX/ PDF should be produced for PeerJ submission
and archiving at the PeerJ preprint server.
The examples for DOCX/ ODT are kept relatively simple, to show the proof-of-principle
and to provide a plain document for the development of own templates. Nevertheless, the
generated documents should be suitable for submission after little manual editing. For
specific journals it may be necessary to create more sophisticated templates or to copy/
paste the generic DOCX/ ODT output into the publisher’s template.
Development of a DOCX/ ODT template
A first DOCX document with bibliography in PLoS format is created with Pandoc DOCX
output:
pandoc -S -s --csl=plos.csl --filter pandoc-citeproc
-o pandoc-manuscript.docx agile-editing-pandoc.md
The parameters -S -s generate a typographically correct (dashes, non-breaking spaces
etc.) stand-alone document. A bibliography with the PLoS style is created by the citeproc
filter setting --csl=plos.csl --filter pandoc-citeproc.
The document settings and styles of the resulting file pandoc-manuscript.docx can be
optimized and be used again as document template
(--reference-docx=pandoc-manuscript.docx): instead of .
pandoc -S -s --reference-docx=pandoc-manuscript.docx --csl=plos.csl
--filter pandoc-citeproc -o outfile.docx agile-editing-pandoc.md
It is also possible to directly re-use a previous output file as template (i.e., template and
output file have the same file name):
pandoc -S -s --columns=10 --reference-docx=pandoc-manuscript.docx
--csl=plos.csl --filter=pandoc-citeproc
-o pandoc-manuscript.docx agile-editing-pandoc.md
In this way, the template can be incrementally adjusted to the desired document
formatting. The final document may be employed later as Pandoc template for other
manuscripts with the same specifications. In this case, running Pandoc the first time with
the template, the contents of the new manuscript would be filled into the provided DOCX
template. A page with DOCX manuscript formatting of this article is shown in Fig. 8.
The same procedure can be applied with an ODT formatted document.
Krewinkel and Winkler (2017), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.112 17/23
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http://dx.doi.org/10.7717/peerj-cs.112
Figure 8 Opening a Pandoc-generated DOCX in Microsoft Office 365.
Development of a TEX/PDF template
The default Pandoc LATEX template can be written into a separate file by:
pandoc -D latex > template-peerj.latex
This template can be adjusted; for example, by defining Unicode encoding (see above), by
including particular packages or setting document options (line numbering, font size). The
template can then be used with the Pandoc parameter --template=pandoc-peerj.latex.
The templates used for this document are included as Supplemental Material (see section
‘Software and Code Availability’ below).
Styles for HTML and EPUB
The style for HTML and EPUB formats can be defined in .css stylesheets. The Supplemental
Material (see section ‘Software and Code Availability’ below) contains a simple example
.css file for modifying the HTML output, which can be used with the Pandoc parameter
-c pandoc.css.
AUTOMATING DOCUMENT PRODUCTION
The commands necessary to produce the document in a specific formats or styles can be
defined in a simple Makefile. An example Makefile is included in the source code of
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http://dx.doi.org/10.7717/peerj-cs.112
Table 3 Relevant software used for this article.
Software Use Authors Version Release Homepage/repository
Pandoc Universal markup
converter
John MacFarlane 1.16.0.2 16/01/13 http://www.pandoc.org
Pandoc-citeproc Library for CSL citations
with Pandoc
John MacFarlane,
Andrea Rossato
0.9.1 16/03/19 https://github.com/jgm/
pandoc-citeproc
Pandoc-jats Creation of JATS files
with Pandoc
Martin Fenner 0.9 15/04/26 https://github.com/
mfenner/pandoc-jats
ownCloud Personal cloud software ownCloud GmbH,
Community
9.1.1 16/09/20 https://owncloud.org/
Markdown Editor Plugin for ownCloud Robin Appelman 0.1 16/03/08 https://github.com/
icewind1991/files_
markdown
BibTool Bibtex database tool Gerd Neugebauer 2.63 16/01/16 https://github.com/ge-
ne/bibtool
this article. The desired output file format can be chosen when calling make. For example,
make outfile.pdf produces this article in PDF format. Calling make without any option
creates all listed document types. A Makefile producing DOCX, ODT, JATS, PDF, LATEX,
HTML and EPUB files of this document is provided as Supplemental Material (see section
‘Software and Code Availability’ below).
Cross-platform compatibility
The make process was tested on Windows 10 and Linux 64 bit. All documents—DOCX,
ODT, JATS, LATEX, PDF, EPUB and HTML—were generated successfully, which
demonstrates the cross-platform compatibility of the workflow.
PERSPECTIVE
Following the trend to peer production, the formatting of scientific content must become
more efficient. Markdown/Pandoc has the potential to play a key role in the transition
from proprietary to community-driven academic production. Important research tools,
such as the statistical computing and graphics language R (R Core Team, 2014) and the
Jupyter notebook project (Kluyver et al., 2016) have already adopted the MD syntax (for
example, http://rmarkdown.rstudio.com/). The software for writing manuscripts in MD is
mature enough to be used by academic writers. Therefore, publishers also should consider
implementing the MD format into their editorial platforms.
CONCLUSIONS
Authoring scientific manuscripts in markdown (MD) format is straight-forward, and
manual formatting is reduced to a minimum. The simple syntax of MD facilitates document
editing and collaborative writing. The rapid conversion of MD to multiple formats such as
DOCX, LATEX, PDF, EPUB and HTML can be done easily using Pandoc, and templates
enable the automated generation of documents according to specific journal styles.
Krewinkel and Winkler (2017), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.112 19/23
https://peerj.com
http://www.pandoc.org
https://github.com/jgm/pandoc-citeproc
https://github.com/jgm/pandoc-citeproc
https://github.com/mfenner/pandoc-jats
https://github.com/mfenner/pandoc-jats
https://owncloud.org/
https://github.com/icewind1991/files_markdown
https://github.com/icewind1991/files_markdown
https://github.com/icewind1991/files_markdown
https://github.com/ge-ne/bibtool
https://github.com/ge-ne/bibtool
http://rmarkdown.rstudio.com/
http://dx.doi.org/10.7717/peerj-cs.112
The additional features we implemented facilitate the correct indexing of meta
information of journal articles according to the ‘semantic web’ philosophy.
Altogether, the MD format supports the agile writing and fast production of scientific
literature. The associated time and cost reduction especially favours community-driven
publication strategies.
SOFTWARE AND CODE AVAILABILITY
The relevant software for creating this manuscript used is cited according to (Smith, Katz
& Niemeyer, 2016) and listed in Table 3. Since unique identifiers are missing for most
software projects, we only refer to the project homepages or software repositories:
ACKNOWLEDGEMENTS
We cordially thank Dr. Gerd Neugebauer for his help in creating a subset of a bibtex data
base using BibTool, as well as Dr. Ricardo A. Chávez Montes, Prof. Magnus Palmblad and
Martin Fenner for comments on the manuscript. Warm thanks also go to Anubhav Kumar
and Jennifer König for proofreading.
ADDITIONAL INFORMATION AND DECLARATIONS
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.
Grant Disclosures
The following grant information was disclosed by the authors:
Consejo Nacional de Ciencia y Tecnología (CONACyT).
FRONTERAS 2015-2/814.
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
(CINVESTAV).
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 and 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.
Krewinkel and Winkler (2017), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.112 20/23
https://peerj.com
http://dx.doi.org/10.7717/peerj-cs.112
Data Availability
The following information was supplied regarding data availability:
The software created as part of this article, Pandoc-scholar, is suitable for general
use and has been published at https://github.com/pandoc-scholar/pandoc-scholar;
10.5281/zenodo.376761. The source code of this manuscript, as well as the templates and
Pandoc Makefile, have been deposited to https://github.com/robert-winkler/scientific-
articles-markdown/.
Drawings for document types, devices and applications have been adopted from Calibre
(http://calibre-ebook.com/), openclipart (https://openclipart.org/) and the GNOME
Theme Faenza (https://code.google.com/archive/p/faenza-icon-theme/).
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FURTHER READING
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hybrid publishing toolkit for the arts. Amsterdam: Institute of Network Cultures.
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