PDF Annotation Extractor

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A Workflow for Alfred to extract annotations as Markdown file. Primarily for scientific papers, but can also be used for non-academic PDF files.

Automatically determines correct page numbers, inserts them as Pandoc citations, merges highlights across page breaks, prepends a YAML header with bibliographic information, and more.

Installation
Requirements for the PDF
- Automatic citekey identification
Usage
Troubleshooting
Cite this software project
Credits
About the Developer

Installation

Requirement: Alfred 5 with Powerpack
Install Homebrew
Install pdfannots2json by running the following command into your terminal: brew install mgmeyers/pdfannots2json/pdfannots2json
Download the latest release.
Set the hotkey by double-clicking the sky-blue field at the top left.
Set up the workflow configuration inside the app.

Requirements for the PDF

PDF Annotation Extractor works on any PDF that has valid annotations saved in the PDF file. Some PDF readers like Skim or Zotero 6 do not store annotations in the PDF itself by default.

This workflow automatically determines the citekey of based on the filename of your PDF file.

If the citekey is found, the PDF Annotation Extractor prepends a yaml header to the annotations and automatically inserts the citekey with the correct page numbers using the Pandoc citations syntax.
If your filename does not contain citekey that can be found in your library, the PDF Annotation Extractor extracts the annotations without a yaml header and uses the PDF numbers as page numbers.

Automatic citekey identification

The filename of the PDF file MUST begin with the citekey (without @).
The citekey MUST NOT contain any underscores (_).
The name of the file MAY be followed by an underscore and some text, such as {citekey}_{title}.pdf. It MUST NOT be followed by anything else, since then the citekey would not be found.
Example: With the filename, Grieser2023_Interdependent Technologies.pdf, the identified citekey is Grieser2023.

[!TIP] You can achieve such a filename pattern with automatic renaming rules of most reference managers, for example with the ZotFile plugin for Zotero or the AutoFile feature of BibDesk.

Usage

Basics

Use the hotkey to trigger the Annotation Extraction on the PDF file currently selected in Finder. The hotkey also works when triggered from PDF Expert or Highlights. Alternatively, use the anno keyword to search for PDFs and select one.

Annotation Types extracted

Highlight ➡️ bullet point, quoting text and prepending the comment as bold text
Free Comment ➡️ blockquote of the comment text
Strikethrough ➡️ Markdown strikethrough
Rectangle ➡️ extracts image and inserts Markdown image link at the respective place
Underlines ➡️ sent to Reminders.app as a task due today in the default list

Automatic Page Number Identification

Instead of the PDF page numbers, this workflow retrieves information about the real page numbers from the BibTeX library and inserts them. If there is no page data in the BibTeX entry (for example, monographies), you are prompted to enter the page number manually.

In that case, enter the real page number of your first PDF page.
In case there is content before the actual text (for example, a foreword or Table of Contents), the real page number 1 often occurs later in the PDF. If that is the case, you must enter a negative page number, reflecting the true page number the first PDF would have. Example: Your PDF is a book, which has a foreword, and uses roman numbers for it; real page number 1 is PDF page number 12. If you continued the numbering backwards, the first PDF page would have page number -10, you enter the value -10 when prompted for a page number.

Annotation Codes

Insert the following codes at the beginning of an annotation to invoke special actions on that annotation. Annotation codes do not apply to strikethroughs.

+: Merge this highlight with the previous highlight or underline. Works for annotations on the same PDF-page (= skipping text in between) and for annotations across two pages.
- ? foo (free comments): Turns "foo" into a Question Callout (> ![QUESTION]) and move up. (Callouts are Obsidian-specific Syntax.)
##: Turns highlighted text into a heading that is added at that location. The number of # determines the heading level. If the annotation is a free comment, the text following the # is used as heading instead. (The space after the is # required).
=: Adds highlighted text as tags to the YAML frontmatter. If the annotation is a free comment, uses the text after the =. In both cases, the annotation is removed afterward.
_: A copy of the annotation is sent Reminders.app as a task due today (default list).

[!TIP] You can run the Alfred command acode to display a cheat sheet of all annotation codes.

Extracting Images

The respective images are saved in the attachments sub-folder of the output folder, and named {citekey}_image{n}.png.
The images are embedded in the markdown file with the ![[ ]] syntax, for example ![[filename.png|foobar]]
Any rectangle type annotation in the PDF is extracted as image.
If the rectangle annotation has any comment, it is used as the alt-text for the image. (Note that some PDF readers like PDF Expert do not allow you to add a comment to rectangular annotations.)

Troubleshooting

Update to the latest version of pdfannots2json by running brew upgrade pdfannots2json in your terminal.
This workflow does not work with annotations that are not actually saved in the PDF file. Some PDF Readers like Skim or Zotero 6 do this, but you can tell those PDF readers to save the notes in the actual PDF.

[!NOTE] As a fallback, you can use pdfannots as extraction engine, as a different PDF engine sometimes fixes issues. This requires installing pdfannots via pip3 install pdfannots, and switching the fallback engine in the settings. Note that pdfannots does not support image extraction and the extraction quality is slightly worse, so generally you want to use pdfannots2json.

Cite this software project

If you want to mention this software project in an academic publication, please cite it as:

Grieser, C. (2023). PDF Annotation Extractor [Computer software]. 
https://github.com/chrisgrieser/pdf-annotation-extractor-alfred

For other citation styles, use the following metadata:

Credits

To Andrew Baumann for pdfannots, which caused me to develop this workflow (even though it does not use pdfannots anymore).
Also, many thanks to @mgmeyers for pdfannots2json, which enabled many improvements to this workflow.
I also thank @StPag for his ideas on annotation codes.
Icons created by Freepik/Flaticon

About the Developer

In my day job, I am a sociologist studying the social mechanisms underlying the digital economy. For my PhD project, I investigate the governance of the app economy and how software ecosystems manage the tension between innovation and compatibility. If you are interested in this subject, feel free to get in touch.

chrisgrieser / pdf-annotation-extractor-alfred

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