The Bookends Format
I created a Format (called Obsidian Export) that collects the information that I want. Here is the format statement for a journal article.
Code: Select all
$## Article $u1
t; a
j $**$v$**$(i) p (d)
$### Notes$
$*Label*$ &
n
$### Links$
$https://doi.org/${u17^ }
$$
%
* The u1 output is the citation key used in the level 2 header to mark the note
* The links section has both the DOI and a reference to the PDF file itself. The latter is specifically pointing to a file in a specific sub-directory. That sub-directory is bibliographies/THELIBRARYNAME
An Example Format for a Reference
Here is an example of the output for a specific reference in my Functionalize library.
Code: Select all
## Article Qi2009
Simple Approach to Wafer-Scale Self-Cleaning Antireflective Silicon Surfaces; Qi, D et al.
Langmuir **25**(14) 7769 (2009)
### Notes
*Label* no label
#how provides a recipe to deposit fluorosilane in toluene with wet chemistry
### Links
https://doi.org/10.1021/la9013009
I created a SYMLINK (not an alias) for my Attachments/Functionalize library from Bookends. I put this SYMLINK into the Obsidian vault folder and remove the SYMLINK term on the name. This gives Obsidian direct access to all files in the Bookends Library.
- Obsidian SYMLINK
- Obsidian SYMLINK.png (48.2 KiB) Viewed 35986 times
- Obsidian Vault
- Obsidian Vault.png (76.45 KiB) Viewed 35986 times
To obtain a report, I run the menu Export References or Bibliography. I use the Obsidian Export format to output to a Plain Text (ASCII) file on Disk. Save the file with an .md file extension. Put the report into the bibliographies directory in the Obsidian vault.
Example Report in Obsidian
Here is an example report in Obsidian. I have exposed only the reference that is shown in the above code section.
- Obsidian Report
- Obsidian Report.png (89.46 KiB) Viewed 35986 times
The next steps are to post my entire Functionalize library to a Google Drive folder, to provide instructions to my colleagues on how to set up Obsidian for use. After this, I can post snap-shot reports with my comments to articles using the Notes section. My colleagues should only need to put the report in their bibliographies section to see the report and to access the related PDF file directly.
Caveats and Improvements
I use the #tag format in notes for tags. If you use the Bookends default %tag format, you will have to do some post-processing to convert those to #tag formats to be recognized in Obsidian. Note also that Obsidian demands #(SPACE)Header formats for headers while Bookends outputs markdown headers internally as #Header (no space). Finally, I would wish (and have asked) that formats can have access to Finder tags so that I could include them also in the Notes portion of the report. For example, I use a Finder tag "annotated" on PDFs that I markup as a way to track this at a system-wide level (e.g. also in Devonthink).
I hope this initial posting finds some use.
