Citations and bibliography

[melsophos]

@argentum

My intention is not to bother you, I am trying to explain the difficulties of what you’re asking. I can see where you are coming from, but it’s considerably hard (at least for me) to imagine a solution which doesn’t require reference management, but provides you all the citation capabilities you want.

I appreciate having other inputs, I think it’s important to refine the idea. Overall, having pure Pandoc + literature note linking as explained in the other FR would satisfy 95% of my needs. Having the possibility to complement the bibliography by hand in the file itself would be great, but not imperative. However, I am not sure to see why it would be hard. And sorry about the tone, I got a bit irritated because I had the impression to explain several times the same thing, especially that I want to avoid as many actions as possible with Zotero because it is SO slow and I am already loosing so much time with this.

Indeed, you can have a reference section at the end of the markdown file with a few references not present in the bibliography file. These items could be formatted as:

[@notinbib]: Smith. “An amazing work”.

and I can use [@notinbib] to cite in the text, along with any other item present in the bibtex file., say [@inbib]. Now for the preview / export, Pandoc is first called to generate the bibliography from the bibtex file as usual, and it inserts it in the reference section (let’s say that there are 17 such items). Then we process by hand the remaining citation, replacing [@notinbib] by [18] in the text, and then append to the Pandoc-generated list all remaining items. Obviously, this works well for number-based citations, less for name-based citation, but I am sure we can come up with some heuristics/convention.

Also let me re-say a motivation for this: someone may not want to use a reference management software and just cite a few things in some notes, in which case having a simpler system may be appreciated.

I admit it starts to be specialized, so I could imagine this being done by a plugging and not in Obsidian’s core itself (which would process online pure Pandoc, following @WhiteNoise suggestion). The only thing is that the bibliography generation should allow for a way to intervene and reprocess/add references to the list with plugins.

@argentum

By the way, if you are using Better BiBTeX with Zotero I would recommend generating smaller bib files (e.g. by exporting them from a collection). I think probably you’re not citing all 13k of them in obsidian, but even if you are, smaller bib files most likely will help you there. Another option is to have a separate profile for your casual web linking citations: kb:multiple profiles [Zotero Documentation]

Thanks for the suggestions. Now I am using a collection “Obsidian” where I am moving only what I may use in Obsidian. The only problem is that I have to think in advance what I will likely write on, and this adds some micro-management (moreover, because of the lag problem I mentioned, moving one item blocks Zotero for a few seconds, so it’s painful to move several documents one after this other). I had not thought of using two profiles: I have to think about it, although I fear that it would require too much shifting.

[alltagsverstand]

@melsophos does it help if you change your betterbibtex auto-export preferences from “on change” to “when idle”? This would prevent the betterbibtex plugin from processing a huge bib file each time you change a single letter in zotero - it would rather work in the background as soon as you switch back to obsidian or any other app…

[atiz]

Just my 2 cents: learning how to use BibDesk was by far the best time investment in my academic life, and learned pretty early on that a central bib database is really the only way to go.
You may think that it’s not worth bothering with putting in a reference used only once. But you never know down the line if you’re going to use it again, and having to search for it in multiple places and in notes is just annoying (at least it was for me – have done my fair share of these things too).
Of course YMMV.

[melsophos]

@alltagsverstand

@melsophos does it help if you change your betterbibtex auto-export preferences from “on change” to “when idle”? This would prevent the betterbibtex plugin from processing a huge bib file each time you change a single letter in zotero - it would rather work in the background as soon as you switch back to obsidian or any other app…

I am using “manually” to have full control on when it is done. I never tried “on idle” since I was not sure of when it would be triggered but maybe I can try. Thanks for suggesting!

[greglh]

I am new to the Obsidian community and this is my first post. So, I am very humbly offering my thoughts here as a point-of-view. I do so because I have a keen interest and hope for using obsidian as a knowledge-content management “tool” in a workflow spanning from post-capture of a reference source into ref mgmt syst (Zotero in my case), to the point of publishing articles, books and web content — all with content continuity.

I come from the Scrivener, Notion, Roam Research worlds as a reference point with great hope Obsidian intends to become such a tool on the longer end.

My attraction to Obsidian is its plain text, local file, interlinking knowledge graph design center for all the many reasons these are valuable, and these are the decisive reasons that warrant the investment of time differentially into learning, using and helping to advance the dev of Obsidian.

The paramount goal for me, and perhaps others here, is to end up possess a “knowledge-content creation workflow management system” on the long-end. The attraction to Obsidian in it having the base attributes mentioned above, and the potential for becoming such a system spanning functionality from content capture, to coding (classifying, tagging), content revision and maintenance, content inter-linking, content exploration, analysis and publishing.

This would mean Obsidian supporting a workflow that can would:

• continuously build up a universally useful and accessible inter-linked, content-classified personal-professional knowledge-graph, and in so being
• provide a tool useful for doing productive knowledge processing, content creation in service to our personal and career work needs
• provide note functionality across the entire knowledge-content workflow from ideation to content analysis, creation and publishing of ongoing works, in all contemporary forms.

Note taking is vital to this, but hardly a “whole-product” solution or platform.

As a result, IMHO there are a couple of points in this discussion that while notable for being valid, seem vector away from clearly inform Obsidian development objectives in regard to WHAT independent of HOW:

@argentum

I don’t think Obsidian should replace the functionality of a reference manager. While I understand that some like to have everything under a single app, note-taking and reference management are two very different apps with very different needs.

• Argentum, I believe you are 100% correct in saying that Obsidian should not seek to build and become a replacement for current reference management apps
• However, needing Obsidian to be a note taking and using app that is low friction, productive and value-adding in using and syncing content that exists in reference mgmt and other apps critical to meet user content-knowledge management workflow, is another matter.
• Yes, the needs of note-taking and reference management are different, but both are essential needs within any users singular but broader workflow.

Please forgive me for applying the metaphor, that if one needs and wants a hole put into something “to do their real work,” then that alone is the reason they will or should buy and use a drill. Obsidian is a drill. Therefore, creating and getting notes, citations, et al. into Obsidian is not the end goal, nor does the content used in our workflows, start or end in Obsidian.

Moving content through obsidian from external input to external use and end points of our workflow, effectively and efficiently, defines (in my view) the primary function of Obsidian or any such note-taking tool. This being even more so true for Obsidian because they are developing knowledge-graph functionality, and their revenue and business model is dependent upon the publishing end of such workflows.

@argentum

I am trying to explain the difficulties of what you’re asking. I can see where you are coming from, but it’s considerably hard (at least for me) to imagine a solution which doesn’t require reference management, but provides you all the citation capabilities you want.

In the end, I think this actually makes the point I am trying to highlight, indicating that for any next generation note taking tool to fill real world user needs, means doing so within real world user workflows. Especially those that lead to publishing. It would seem then that any such app logically be able to pull, use-modify and output not just reference management content and metadata. But, also do the same more broadly to and from apps that perform qualitative and statistical data analysis and others function needed by and before the publishing and presentation stage.

[crystalatom]

I spent some time to follow this thread about Zotero/Bibliography and two workflows: one using Zotero/MDNotes/Dataview and the other using obsidian-citation and I agree with @melsophos that neither is perfect and we need an unifying solution. I do like the idea of exporting each reference as a separate note and use dataview to aggregate the bibliography. Here is what’s better with MDNotes compared to citations, because it resides inside Zotero:

1. More metadata can be exported, e.g. the authors can be listed individually in wiki link format.

but the issue with MDNotes is that:

1. MDNotes does not update the exported notes automatically;
2. MDNotes is not flexible enough in setting the template, whereas dataview only reads YAML header or inline field defined with ::.
3. There are many issues using YAML header for metadata, for example, some titles include : as part of the title, which will break the YAML parser.

The bibliography is a pain I still struggle with between Obsidian and Zettlr.

[argentum]

@crystalatom

• MDNotes is not flexible enough in setting the template, whereas dataview only reads YAML header or inline field defined with ::.
• There are many issues using YAML header for metadata, for example, some titles include : as part of the title, which will break the YAML parser.

You can customize templates as much as you want to achieve that, see: https://argentinaos.com/zotero-mdnotes/docs/next/advanced/formatting

[crystalatom]

Thanks, figured it out finally that I need to use the 0.2 alpha