[DanielBMarkham]

I'll try.

1. What are you trying to do? If it's simple research off the web, simply copy some files and paste, or use MarkDownload and get fully formed markdown from a page to put in your vault.

2. Can you code? You don't need to code, but things make a lot more sense in Obsidian if you know markdown, CSS, and maybe a bit of javascript/html. I didn't use anything but markdown productively for a long time. Even now there's very few plugins I would recommend. ADD: When I started, I went through all the plugins and added everything under the sun. This is because I was stupid and thinking I was at some kind of nerd buffet. Once I realized I was looking at complexity upside down, Obsidian kicked ass.

Your second issue is a feature for me, so I can't help there.

As to your specific question, if you're stuck on Zotero, then add stuff there and make a one-way pipeline to Obsidian. Obsidian becomes your source of truth. If not, ditch it. I don't think it does anything Obsidian doesn't, but you should check with some users.

Remember KISS, Keep It Simple, Silly. One tool. If you're stuck using two tools, one-way data pipelines. Syncing two knowledge tools together sounds like a nightmare and I'd stop doing that right away.

One more thing: I decided on folders for long-term categorization, things I think will mostly never change. Then tags, nested tags specifically, for trying to freeform WTF I'm doing. Tag Wrangler is awesome for this. There are only about five extensions I'd always use. Tag Wrangler is one of them.

[kens]

Thanks for your reply. For background, I'm doing technical/historical research. I have 100 documents on a topic (mostly PDFs, also some scans) and I want to keep track of them, pull ideas out of them, and write a coherent article. Cut-and-paste isn't enough at this point. Zotero is the perfect solution for me to keep source documents organized and I would pay money to keep using it. Researchers who use Obsidian mostly use Zotero too (it seems) since Obsidian doesn't handle citation management, tracking documents, downloading, OCR, PDF annotation, and other important tasks.

For your second point, sure, I can write tons of code. That's why I'm cautious with Obsidian; I don't want to get distracted by writing templates and JavaScript customization rather than useful work.

By the way, the basic Obsidian process I'm using is "Notetaking for historians", which is described at https://publish.obsidian.md/history-notes/01+Notetaking+for+... This process is very similar to the process described in the topic article.

[DanielBMarkham]

My first Obsidian project was a research project for an upcoming non-fiction book. It's not academic, but I believe the synthesis/citing issue is generally the same.

I just looked at it. It has a little over 1,000 files in it, so I've been filing a lot.

I only have dataview, PDF to markdown, templater, and a couple other community plugins enabled. My decision was to dump everything, kit-and-kaboodle, into a Reference folder. No processing, no tagging, just dump it in there. Then I created a Topic Summaries and a Synthesis folder. The idea here is not to start categorizing and synthesizing until you're absolutely forced to.

Between Topic Summaries and Synthesis I create a book outline. Note that the folder names are things that are set in concrete. Then I created a tag system. As I begin teasing out ways to organize my research, simultaneously I create a tagging system. So one research item may eventually get referenced in several Synthesis Notes. I may go back and create a Topic Summary based on the syntheses or just ad-hoc. The tagging system links to that layer, not the data dump layer.

This allows me to continue dumping data, then join it up in various creative ways later. I don't even hook my synthesis into an outline directly. That's a separate and also creative step. Once joined and I've committed to an outline, I can chase down the original research and provide whatever footnotes or links I feel are appropriate.

Hope that helps. My big lesson was not to categorize my research as I gathered it. Usually my first guess is wrong. Instead use an abstraction layer and continue to churn through synthesizing many docs into new ideas. Then join those ideas into an outline.

Best of luck.