New publication in International Journal of Digital Libraries

| categories: news, publication | tags:

We have a new paper out on using org-mode in publishing. The idea is to use org-mode to automate data embedding in publications. For example, in org-mode tables can serve as data sources. We show how you can automatically embed the tables as csv files in PDF or HTML when the org-file is exported. Similarly, all the code blocks are embedded as extractable files at export time. This increases the reusability of the data and code in papers.

Check out the preprint here:

  author =       "Kitchin, John R. and Van Gulick, Ana E. and Zilinski, Lisa D.",
  title =        "Automating data sharing through authoring tools",
  journal =      "International Journal on Digital Libraries",
  year =         "2016",
  pages =        "1--6",
  abstract =     "In the current scientific publishing landscape, there is a
                  need for an authoring workflow that easily integrates data and
                  code into manuscripts and that enables the data and code to be
                  published in reusable form. Automated embedding of data and
                  code into published output will enable superior communication
                  and data archiving. In this work, we demonstrate a proof of
                  concept for a workflow, org-mode, which successfully provides
                  this authoring capability and workflow integration. We
                  illustrate this concept in a series of examples for potential
                  uses of this workflow. First, we use data on citation counts
                  to compute the h-index of an author, and show two code
                  examples for calculating the h-index. The source for each
                  example is automatically embedded in the PDF during the export
                  of the document. We demonstrate how data can be embedded in
                  image files, which themselves are embedded in the document.
                  Finally, metadata about the embedded files can be
                  automatically included in the exported PDF, and accessed by
                  computer programs. In our customized export, we embedded
                  metadata about the attached files in the PDF in an Info field.
                  A computer program could parse this output to get a list of
                  embedded files and carry out analyses on them. Authoring tools
                  such as Emacs + org-mode can greatly facilitate the
                  integration of data and code into technical writing. These
                  tools can also automate the embedding of data into document
                  formats intended for consumption.",
  issn =         "1432-1300",
  doi =          "10.1007/s00799-016-0173-7",
  url =          ""

Copyright (C) 2016 by John Kitchin. See the License for information about copying.

org-mode source

Org-mode version = 8.3.4

Discuss on Twitter