My planing workflow is collecting PDFs on zotero, annotate them on default pdf reader. After reading finished, extract annotations from pdfs by the help of zotfile in Zotero. And use this annotations to write new article. It should be ideal to copy this excerpts ( with linked to pdf in zotero) paste to obsidian and make new notes for each pdf or may be for each annotations. Then while writing use this notes to develop ideas. And if it is possible with new obsdian version, insert reference through ( bibtext addon of zotero) .bib file into obsidian. At the end stage manuscript, styling reference depending on journal with .css styling styles. After all, print as pdf or word files.
Best part of creating this annotation as a note is, you can easliy convert to them permenant or zettel notes ( my suggestion even this notes can be different color to recognize easily ). After 2 or 3 year later you will have a great library to write. By this way you learn more from your read past article also you dont need to read the same article again and again.
Zotero is best for our purpose because it open source, free, annotations have links ( which is very important feature, because after 2 year you want to read this article pdfs so by clicking the link in your permenant note and open the pdf) and betterbibtex addons which is ideal for reference insertion to the markdown files.
To be honest, Zettlr have similar features but dont have graph view. And I think obsidian note system is much better. I hope it will become more excellent with plugins.
I dont know may be my workflow is not so good but may be we can learn more if other users also share their workflows. I hope Obsidian become better than other markdown wiriting tools.
I also suggested Anki plugin especially to memorize some notes easly.
Some links may be helpful