--- title: "Markdown bibliographic referencing workflow" date: "2023-07-14T20:21:29+03:00" author: "anybody" contributors: ["constantinos-miltiadis.md"] draft: false keywords: - guide - markdown guide abstract: | This article outlines a workflow for incorporating bibliographic citations/references in Markdown documents, and exporting new documents with compiled bibliographies according to specific citation styles. All tools involved in this pipeline are free, open source, and cross platform. --- [Better Bibtex]: https://retorque.re/zotero-better-bibtex/ "an extension for Zotero for managing bibliographic data, especially for text-based document authoring toolchains" [Zotero]: https://www.zotero.org/ "free and open source, cross-platform citation management software." [Pandoc]: https://pandoc.org/ "universal document converter" # Introduction This guide outlines a workflow for incorporating bibliographic referencing (citations and references) in ![Markdown](article:md-formatting) documents. The general idea is incorporating citation keys from a bibliography in a Markdown document, and then rendering citations and references by generating a new document against a bibliographic collection (`bib` file), and a citation style (`csl` file). The steps described in the following are: 1. Installing required tools and software; 1. creating and exporting a bibliography collection with [Zotero][]; 2. using citation keys in a Markdown document; 3. getting a citation style file; 4. exporting new documents (e.g. PDF, DOCX, MD, etc.) with [Pandoc][], where citations and bibliographic references are formatted as per any specific citation style. All tools involved in this workflow are free, open source, and cross-platform. --- Note: A *citation* is used in the body of the text to refer to some external source. A *reference* is placed in the "References" or "Bibliography" section of the document providing the full information for a citation. Citations and references are formatted according to a citation style. For example, for an 'author-year' citation style like *Chicago* in-text citations look like: Khaled et al. (2018), or (Khaled et al. 2018). According to the same citation style, the reference for that citation is: - Khaled, Rilla, Jonathan Lessard, and Pippin Barr. ‘Documenting Trajectories in Design Space: A Methodology for Applied Game Design Research’. In _Proceedings of the 13th International Conference on the Foundations of Digital Games_, 1–10. Malmö Sweden: ACM, 2018. [https://doi.org/10.1145/3235765.3235767](https://doi.org/10.1145/3235765.3235767). # Requirements 1. Some Markdown editor for authoring Markdown documents (see ![Markdown guide](article:md-formatting)). 2. [Zotero][] -- free and open source cross platform citation management software. 3. [Better Bibtex][] -- "an extension for Zotero ... that makes it easier to manage bibliographic data, especially for people authoring documents using text-based toolchains (e.g. based on [LaTeX](https://www.latex-project.org/) / [Markdown](https://www.markdownguide.org/)"). 4. [Pandoc][] -- "universal document converter"; command line tool for converting between different document formats (e.g. Markdown, PDF, DOCX, epub, etc.), and compiling bibliographic references. ## Pandoc installation & upgrade {#pandoc-install} [Chocolatey]: https://chocolatey.org/ "Free and open source package manager for Windows." [Homebrew]: https://brew.sh/ "Free and open source package manager for macOS." Pandoc is a command line tool that can be installed via a downloadable installer or through the terminal (see [Installing pandoc](https://pandoc.org/installing.html)). To check if pandoc is installed, and which version is installed, open a terminal and do: ``` pandoc --version ``` If pandoc is not recognized as a valid command, go ahead and install pandoc. Otherwise, upgrade pandoc to the latest release. ### Installation Installing via a terminal requires a package manager (e.g. [Chocolatey][] for Windows, or [Homebrew][] for macOS). - For Windows, using the package manager [Chocolatey] do: ``` choco install pandoc ``` - For macOS, using the package manager [Homebrew][], do: ``` brew install pandoc ``` ### Upgrade To upgrade [Pandoc][], if it was installed via an installer, download and run the latest installer. If it was installed via terminal, it can be upgraded with a single command. - For Windows: ``` choco upgrade pandoc ``` - For macOS: ``` brew upgrade pandoc ``` Verify the version of your Pandoc installation with the command: ``` pandoc --version ``` # Create and export a bibliography collection This section outlines how to create a bibliography collection in Zotero and export it to a `bib` file. 1. In Zotero, create a new collection (titled say `mycollection`). 2. Add to your collection all items you want to reference (by drag and drop to collection, or right click > Add to Collection). 3. With [Zotero][] and [Better Bibtex][] installed, each entry in your Zotero database should have a unique citation key displayed at the top of its Info section (image below). Use this key as in `@key` (or `@khaled2018`) to cite this item in your Markdown document ([further instructions below](#cite)). ![](/markdown-guide/zotero-citation-key.png) 4. To export your reference collection, select the collection, right-click > Export Collection, select **Better BibLaTeX** (uncheck all options; background export optional): ![](/markdown-guide/zotero-export-options.png) 3. Save your collection (e.g. `mycollection.bib`). The resulting file is a dictionary of citation keys, each with its own citation metadata (you can preview the file with a text editor). Notes: - In case you modified your Zotero collection (e.g. added/removed items or edited existing items), re-export the collection and overwrite the previous `bib` file. - *Opt for the BibLaTeX export format.* The BibTeX export format will omit URLs associated with an entry! - The format of citation keys can be changed in the [Better Bibtex][] preferences (Zotero: Tools > Better BibTex > Open preferences). The format used in this example is `auth.lower+year`. # Using citation keys in Markdown documents {#cite} To add a citation in a Markdown file, just prefix a citation key (from Zotero) with the `@` sign, as in `@khaled2018`. Eventually, as described in the following steps, when the document is compiled (against a bibliography and a citation style), citation keys will be rendered according to the specified citation style, and a bibliographic reference will be added to the bibliography section of the document, per each unique cited document. For author-year type citation styles: - To add parentheses to a reference use square brackets, as in `[@khaled2018]` --> "(Khaled et al. 2018)") - For citing multiple sources at once separate keys with semicolons, as in `[@khaled2018;@graziano2019]` --> "(Khaled et al. 2018; Graziano et al. 2019)" - To supress the author name (in author-date citation styles) do `[-@khaled2018]` eg. "According to Khaled and colleagues [-@khaled2018]" will render as "According to Khaled and colleagues (2018)") - To add a page or a note before or after a citation do `[see @graziano2019, p.125]` --> (see Graziano et al. 2019, p.125) # Get a citation style file (CSL) Use a provided citation style file (CSL), or download one from [the official citation style repository](https://github.com/citation-style-language/styles) (GitHub repository), or from the [Zotero Style Repository](https://www.zotero.org/styles) (search interface). Notes: - [Zotero] includes a few CSL files for popular citation styles. These are located in the `styles` directory of the Zotero Data Directory (Zotero > Edit > Preferences > Advanced > Show Data Directory). - Zotero features a citation style editor (Tools > Style Editor), for modifying existing citation styles if needed. # Gather files and paths The next step is to gather all required files that will be used to compile a new document (Markdown document, citation style, and bibliography files) and make a note of their file paths. In addition, make sure that the path of any image referenced in the Markdown document is correct. Good practices: - Gather your Markdown document, bibliography, and CSL files in the same directory, e.g. `/mydocument/`. - Place images inside a subdirectory, e.g. `/mydocument/graphics/` - Make a subdirectory for exporting documents e.g. `/mydocument/export/` - Avoid using spaces in directory or file names. - It is recommended to write down these paths either in a comment section inside your document, or in a separate text file, as in: ``` ``` Notes: - File paths can be either absolute (e.g. `c:/users/me/some-folder/some-file.md`), or relative (e.g. `/some-folder/some-file.md`). However, for relative paths pandoc commands will need to be executed from the base directory of these relative paths. - An easy way to get the absolute path of a file or directory, is to drag and drop it into a terminal, then select the path that will appear, right click, and copy. - Enclosing file paths within "quotes" is optional. However, doing so can bypass the need for escape characters in cases where file or directory names contain spaces. # Test Pandoc and Markdown document Open a terminal: - first, to check that [Pandoc][] is in order do: ``` pandoc --version ``` If the `pandoc` command is not recognized as valid go to [installation instructions](#pandoc-install). - to test that your Markdown document is in order do (this will not compile the bibliography): ``` For docx export: pandoc "/path/to/mydocument/my-article.md" -o "/path/to/mydocument/export/my-article.docx" or for pdf export: pandoc "/path/to/mydocument/my-article.md" -o "/path/to/mydocument/export/my-article.pdf" or for Markdown export: pandoc "path/to/my-article.md" -o "/path/to/export-document.md" --atx-headers --strip-comments --wrap=preserve -t markdown_mmd --standalone ``` # Compile document with bibliographic references To compile a new document including citations and bibliography add the options: | Pandoc option | Description | |-|-| | `--citeproc` | option for rendering citations/references| |`--csl` |option to specify citation style, followed by the path to the `CSL` file| | `--bib` | option to specify bibliography followed by the path to the `bib` file| To compile to PDF do: ``` pandoc "path/to/myarticle.md" --citeproc --bibliography "/path/to/mycollection.bib" --csl "/path/to/reference-style.csl" -o "/path/to/export-document.pdf" ``` *Note: Conversions to PDF format require a LaTeX installation.* --- To compile to DOCX do: ``` pandoc "path/to/myarticle.md" --citeproc --bibliography "/path/to/mycollection.bib" --csl "/path/to/reference-style.csl" -o "/path/to/export-document.docx" ``` To compile to DOCX using a DOCX document as reference/template add the option: ``` --reference-doc="path/to/reference-document.docx" ``` *Note: Conversions to DOCX format will use Footnotes, not Endnotes.* --- To compile to a new Markdown document (with references) do: ``` pandoc "path/to/myarticle.md" --citeproc --bibliography "/path/to/mycollection.bib" --csl "/path/to/reference-style.csl" -o "/path/to/export-document.md" --atx-headers --strip-comments --wrap=preserve -t markdown_mmd-citations --standalone ``` The additional options | Pandoc option | Description | |-|-| | `--atx-headers` | use common (ATX) formatting for Markdown headings | | `--strip-comments`| remove HTML comments(``) | | `--wrap=preserve` | preserve line wrapping (by default pandoc will introduce line breaks)| | `-t markdown_mmd-citations` | `-t` (to) for specifying output format; ` markdown_mmd-citations` for `markdown_mmd` format *with* citations (by default Markdown exports don't render citations/bibliography)| | `--standalone`| export standalone (will also render frontmatter) | # Common Pandoc compilation errors Pandoc will not compile in case of errors. Some common errors include: - missing/wrong citation keys: [Pandoc][] will list all citation keys that were not found in the supplied bibliography file. Correct any potential citation key misspellings, or recompile your bibliography collection to include the missing citations. - file not found: check file paths - cannot write/open file: Pandoc is not able to overwrite files (such as PDF or DOCX) while they are open by other software. # Pandoc command reference [pandoc options manual]: https://pandoc.org/MANUAL.html#options See also: - [Pandoc demos](https://pandoc.org/demos.html), - [Getting started with pandoc](https://pandoc.org/getting-started.html), and - [pandoc options manual][]. A basic pandoc command example is: ``` pandoc "path/to/input.txt" -o "path/to/output.docx" ``` Additional options can be added to this command pattern to specify export parameters. Here is a brief list of some commonly used pandoc options (enclosing file paths inside quotation marks is optional): |Pandoc option | Description | |- |- | | `-i "path/to/input/file.ext"` | input file, followed by path to file including file extension (usually `-i` is omitted when input file is specified at the beginning of the command)| | `-o "/path/to/output/file.ext"` | output file, followed by path to file, including file extension| | `-f` | (from) for specifying input format, followed by option, see [pandoc options manual][]| | `-t` |(to) for specifying output format, followed by option, see [pandoc options manual][]| | `-s`, `--standalone` | to produce standalone file, which will render title, abstract, keywords, using data from front matter of the Markdown document| | `-C`, `--citeproc` | option to render citations; will expect bibliography and csl files | | `--bibliography "path/to/bibliography.bib"`| specify bibliography file | | `--csl "path/to/citation-style.csl"` |specify citation style file| | `--atx-headers` | use common (ATX) formatting for Markdown headings| | `--wrap=preserve` | option to preserve line wrapping for plain text output formats (other options: `auto`\|`none`)| | `--strip-comments` | remove HTML comments (``)| | `--no-highlight` | Disables syntax highlighting for code blocks and inlines| # Specify bibliography placement By default, [pandoc][] will insert the bibliography at the end of the document. To force the bibliography to render at a specific location if needed -- for example before endnotes or appendix sections -- add the following to the target location for your bibliography: ``` ... article body ... # Bibliography ::: {#refs} ::: # Some other appendix Lorem ipsum. ``` or ``` ... article body ... # Bibliography
# Some other appendix Lorem ipsum. ```