Help me finding a way to create my Academic Workflow

I am planning to transit to Obsidian from OneNote, but I am getting a hard time on trying to figure out a Workflow for my research and PhD work.
Myself: A life science PhD student and Researcher.

Reference management system: Readcube Paper. This is the issue. Most of the workflow are based on Zotero as reference management system.
Why Readcube? I like the web-based app, and it has a good PDF viewer.

I do all the highlighting and annotation in reference manager.

Furthermore, I also use readwise for getting notes from other web-based article including RSS and transferring to obsidian

Planning to use obsidian for a) Note-taking, mostly from Research article read and annotated on my reference management system & RSS reader.
B) Analysing and making notes and generating ideas: Connecting notes using linking and generating ideas
C) Using notes and as original reference to write research papers, articles, and thesis.


  1. How to get annotated notes from reference manager, keeping the link between notes and reference intact. (How can I take advantage of a web-based reference manager ?)

  2. How to get bibliography in to obsidian and use it to cite the notes and article it has created? I can use citation plugin but as per latest update the Windows based Readcube application does not generate an automated .bib file. I can manually take a bib file, but whenever I update my library, I will have to again generate a new bibliography file.

  3. Using PC-based app, I have all the PDF files of my library. How can I take the annotated article PDF files in obsidian and linked it with the bib file and annotation and notes from that article which i have taken from web-based app?(The PDF downloaded by Readcube does not have/show highlights and annotation which I have done in the reference manager itself.)

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