Workflow Example: Bookends (Bibliography Management macOS) -> Obsidian

[DrJJWMac]

This workflow example outlines how to export markdown content from Bookends, a macOS bibliography management app, to Obsidian. This example presumes that you are already somewhat proficient with creating formats as well as extracting and saving PDF annotation in Bookends.

Initial Set Ups

For Bookends

The example uses an Attachments sub-folder Test. You may skip this step and use your full Attachments folder.

Make a symlink (not an alias) to the designated Attachments folder or sub-folder.

Refer to the symlink for the next step.

For Obsidian

This example uses a folder called Bibliography Review. You may use whatever folder you want. Move the above created symlink for the Attachments folder or sub-folder from Bookends into your chosen Obsidian database folder. Remove the symlink suffix.

Generating a Report in Bookends

The Test sub-folder for attachments contains two PDFs. One is annotated (the one that is tagged in blue at the Finder level).

The library database Test.db has imported the two references and marked them for the Hits List.

The Format view pane shows the results for the following Journal Article format titled Markdown Obsidian Full.fmt

$## Article $u1
t; a 
j  v(i) p (d)
$### Links$
$https://doi.org/${u17^ }
$![local file: $h$](<$h$>)$
%
$### Notes$
$*Label*$ &
n
$### Annotations$

Run the File->Extract PDF Annotations menu. An example of selections for this menu is below.

A portion of the extracted report appears as below.

Run the menu File-> Save PDF Annotations to save report to the top level in the folder created in Obsidian (Bibliography Review). Assure that the file has the extension .md (for markdown).

Reviewing the Report in Obsidian

Open Obsidian. You should see the top folder (Bibliography Report) containing the report and attachments folder. In view mode, the report should show the active PDF files. By its delivery through symlinks, the PDF files are actually contained within your Bookends attachments folder or sub-folder.

Conclusion

I hope this example is useful to those who have been using Bookends and Obsidian while longing for a way to bring the two tools into closer harmony.

–
JJW

[swmartin]

DrJJWMac: This looks very useful. What if my PDFs are stored on iCloud, as Bookends seems to require for syncing? I am having trouble with the symlink.

[DrJJWMac]

When you use iCloud with Bookends, the approach I outlined will not work. You have two alternate ways to use Bookends with Obsidian. One is to move to the Bookends WiFi sync instead of Bookends iCloud sync. This keeps your attachments folder local on macOS and iPadOS rather than using iCloud as a shared repository. The other way to work is to set an Obsidian folder for Bookends export, choose a set of references, export the PDF annotations into the Obsidian folder, and export the respective attachments into a subfolder. Some changes would be needed in the .fmt file to assure the links.

Follow ups are better directed to the Bookends forum, where the audience involved may have its own additional insights.

–
JJW

[Mk20]

I wanted to share a somewhat similar workflow that I created using Shorcuts. This one also extracts the notes from a reference and saves them as a note in a specified folder in Obsidian. It does the work of naming and setting the contents of the note in Shortcuts itself, using a mix of Shortcuts actions and applescript, which I found gave me a lot more flexibility. It doesn’t embed the PDF. It’s a little clunky at times and can probably be streamlined, but it works.

Here’s the shortcut: Shortcuts
In the middle it runs another shortcut that helps clean up the notes in a format that is much nicer. Here’s a link to that one: Shortcuts

The resulting note looks something like this (shown in source mode)

u

[swmartin]

This looks really useful and I’m trying it out. I’m not too familiar with Shortcuts, so it’s a bit of a learning curve. Is there a way to get the citation key as well?

[DrJJWMac]

@swmartin

Is there a way to get the citation key as well?

The Bookends code for citation key is u1. Using the Workflow approach that I posted, add u1 to the Bookends format to export. Using the Shortcuts approach, you probably need to insert a directive to tell Bookends to “set theCiteKey to u1 of theReference” or an equivalent.

–
JJW