I have been using Obsidian for most of my works since few years. From simple note taking, creating presentation, and writing manuscript draft. Recently, when I was about to submitting the manuscript in a Latex format, I got several issues related to bibliography.

I did not want to include all items in my Zotero library in the bibtex. I just wanted to use the bibliography that were cited in my manuscript. So, I looked for the solutions through internet and talking with AI copilot. Here is the workflow that works for me.

Extract bibliography

You are going to need the following setup:

• Pandoc version 3.5 above
• Lua filter
• Complete bibliography file extracted from Zotero.

That complete bibliography file enables my Obsidian to cite directly from my Zotero library. To generate this file, you will require to install Better Bibtex plugin in Zotero. It is automatically updated whenever there is an update in the library.

Create a file naming extract-bib.lua with the following code:

function Pandoc(d)
  d.meta.references = pandoc.utils.references(d)
  d.meta.bibliography = nil
  return d
end

Place that file in the same directory with your markdown file. Of course you can put it elsewhere and use relative path. Then run the following command in the command shell.

pandoc --bibliography=[complete-bibliography.yaml] --lua-filter extract-bib.lua manuscript.md --to=bibtex -o references.bib

You can replace complete-bibliography.yaml with the relative path of your bibliography file. In this case, I use yaml type while you may choose different type to extract your Zotero library.

Get DOIs corrected

After the cited bibliography extracted, I found that some of the entries were not conform the requirement of natbib, which is required by the journal to compile the bibtex. For instance, the bibtex contains no DOI entries.

To find DOI automatically using the bibtex, use a python code from this repository https://github.com/ramonium/AutomaDOI.

You can verify the updated DOIs in the bibtex through this website https://www.doi2bib.org.

Reformat bibtex

Sometimes you may encounters another issue related to UTF-8 encoding. This happens when your bib entries contains special characters, like å, ø, æ, inherent in authors’ name. There is no work around for this issue. You need to replace those character with Bibtex-compliant format.

Maybe you can also try to include package to solve it. See https://overleaf.com/learn/latex/International_language_support.

Optional

If you want to reformat the bibtex into biblatex with braces, you can just copy paste those bib entries to the following website:

https://flamingtempura.github.io/bibtex-tidy

Once you click the Tidy button, it will automatically beautify your bib entries.