I am using the Zotlit plugin to cite scientific articles from Zotero with the ‘Insert Markdown citation’ command. In parallel, I use the Pandoc Reference List plugin to have the list of my references in Obsidian.
It works very well for articles that I already had in Zotero. But when I add new articles to my Zotero library, the citation is not found by Obsidian (even when I am refreshing the Zotero database in Obsidian). Obsidian seems to communicate with Zotero because it is able to find the newly added article with the search panel, but it no longer transforms the citation key [@Author2024blablabla] into (Author et al., 2024), and the reference is not added in the Reference list.
Hopefully someone can answer here, but if you use Discord, the Obsidian Members Group #academic-tools channel has lots of info and knowledgable folks willing to help.
Not an active user of this system myself, but pandoc generates the reference list based on a Bibtex bibliographic database. Such database is generated by the BetterBibtex Zotero plugin. My suspicion is that in your case, this (external to Zotero) bibliographic database is not being automatically updated. Another possibility is that you are using a differen bibtex file than that which is generated by Better Bibtex.
So check your Better Bibtex setting, and
Check whether the bibliography you use in Obsidian matches the one generated by Better Bibtex.
Did you try what @vanadium suggested? I have some additional suggestions, if the issue persists, even if you do have the right up-to-date bibliography file linked in Pandoc Reference List.
Hi @vanadium. I have a similar issue and am using your advice to try and fix it. I’m unsure how to do what you are suggesting. How do I check to see if the database is auto updating. Where do I find which bibliography is being used in Obsidian?
As I indicated, I am not an active user of the system myself anymore, but I still have the plugin Better Bibtex installed.
In Zotero, open the menu “Tools” – “Better Bibtex” – “Open Better Bibtex Preferences”
On the “Automatic Export”, you can see which automatic exports you have set up. You see the file path to the exported bibliography displayed in the drop down menu item
If you do not see any export setup, then you will first need to set up an export.
“File” – “Export Library”
In the “Export…” dialog, select the export format of your choice. I have it in “Better CSL YAML”.
If you want the export to be done automatically when you change the Zotero database, check “Keep updated”, and optionally “Background export” so this happens in a background proces.
Hit “OK”. You now see a file dialog that allows you to define directory and name of the exported file.
On the markdown side (pandoc), it is now matter to specify that filename as the library, either in the YAML header or on the command line. Here, I do not have details ready. This can be found in the Pandoc reference information.