Beginning to End Integration Work Flow

1) I'm just beginning to get over the initial learning curve of using Research Rabbit as the academic data/paper collector. It is integrated with zot. What you find in RR can be imported into zot. RR is whole other thing which I won't cover here. It simply works and works well. zot integration is simple.

2) Now in zot you can create what they call in the Obsidian's world 'atomic' notes by creating a zot note FOR EACH highlighted annotation made in zot, as your read the PDF in the new PDF reader in zot.

3) Then in the newly created 'atomic' note (one note for each idea) in zot (now in the note panel) you can add your own notes and tags at the bottom of the quote/highlight from the PDF (again, in the note panel).

NOTE: These tags I speak of are not zot tags. They are a set of tags that I use across RR, zot and Obsidian, for the purpose of having a consistent categorization system. In RR they are used to create folders and subfolders into which papers are added. In zot they are just text strings I add to the bottom of an atomic note which later are used to search and retrieve that note for insertion in MS Word for writing. In Obsidian they become a key player in creating the graphical mind-map (see below). Without this tagging system I don't know how anyone could control hundreds let alone thousands of source documents which exist across applications. A strictly hierarchical system (folder/subfolder) creates a lot of creative friction. Too much time is wasted with your taxonomy and structure. Obsidian allows folders, but the magic is in how you use tags and especially links.

4) The set of atomic notes then can be imported into Obsidian as a single collection set of notes (which you see in the notes panel in zot with the title of "Annotations(date time)"). This will create a single Mark Down file in Obsidian, using author's name, title and date as the name of the MD file. This is default import behavior. This will enable you to put it into an Obsidian folder of author's who write on the same topic. The Obsidian plugin for zot is called Zotero Integration.

5) In obsidian you then break this single multi-note file from zot into finalized atomic notes using your tags added in zot now as obsidian tags. There is an obsidian plugin that does this breaking up into atomic notes (Note Refractor). All of your new atomic notes are automatically linked back to the single note collection (from a single PDF) you imported from zot. The paper (single PDF) will also have ties to all other MD notes (from other papers) based on the tags you used. The import from zot is now an obsidian note with links to all the atomic notes 'refracted' from it. This is the beginning of the power of Obsidian. In time you will have thousands of atomic notes all linking to each other, and you will begin to think differently, when discovering relationships which will add depth to your thinking.

6) As you read papers and make atomic notes in zot, each subsequent paper goes through the same process, and has its own tags. These tags from all of your papers will all be linked to each other in Obsidian, enabling you to see a 'worldview' or 'mind-map' of all of your papers and links via a graph. When you've worked on dozens then hundreds of papers your mind map in Obsidian begins to take shape, and will yield unknown/unthinkable treasures, because your mini-brain can never see the connections that the Obsidian graph will reveal to you. My working style in Obsidian is to use Obsidian folders, tags and links, as well as keywords which are just text I can search for, and are not important enough or too infrequent to promote to a tag. The power of "linking your thinking" as they say in Obsidian's world is a deep dive which can't be covered here.

7) when it comes time to write your paper there are links in obsidian back to the zot based notes in zot, which you originally exported from zot to obsidian.

8) You click on the link in Obsidian (which is automatically created during export from zot), the link takes you back to your zot PDF notes.

9) Then back in zot with the original PDF open, you can see its notes.

10) Now in MS Word (for example) you can execute the Word plugin for zot and chose 'Add Note'. The zot query thing will open and you can search for your keyword/tag which you originally created in zot. The query thing will bring up a list of zot notes with the tag, as well as the first line of the note. This should be enough to find the desired note.

11) After you've insert all of your notes into your writing, you can then create a bibliography in Word as usual using zot.

I think this all works, but admittedly I have not gone through the whole process for publication. I've just tested the pieces.

Why Obsidian? Well it is like sex. You can't explain it to someone who has never experienced it, ditto for RR.

If you see holes in the process let me know.

There is one change to what I mentioned. As dstillman has pointed out elsewhere, you cannot search separately for annotations within a note, if all annotations are combined within a single note. Consequently you would need to keep each annotation as a separate note until a future upgrade where searching within a note (full of annotations) is possible.

Consequently, I am not sure that coming back to zot is what I will be doing. Instead I will likely drag and drop from Obsidian into a word processor when doing my writing. At least that is my thinking for now.

I've heard of logseq. So, why is it preferred by you?

I've become a fan of the concept of 'atomic' notes and 'linking your thinking' graphically, and I have always been very tag oriented, so obsidian seems nature. It has taken me several years to develop my tagging system, which regretfully zot has not as of yet, shown strong interest in revamping how zot uses and maintains tags.

PDF annotations will be visible and searchable in the library view in a later version.

Someday we'll have a single app end to end. For now, I'm finding Obsidian is the better tool for notes management/integration/tagging all with a graphical interface to explore the interconnectedness of my notes. I use zot for the primary repository and PDF reading. Then take the annotations/notes into obsidian to further organize (via links, tags and folders) and to find connections which would be VERY hard to do in zot alone.

Both zot and Obsidian have the ability to link back to the text in the PDF. If you are in the PDF reader in zot the annotations (left panel) will show you where in the PDF an annotation occurs by clicking on the annotation. However, more useful to me is the ability in Obsidian (where I build 'atomic' notes and create links between notes) to be able to go back to the spot in the PDF via zot links if I want to re-read a section.

Obsidian is more that a Citavi-like notes browser. It is that and more.

@bolejj That sounds quite intriguing. Would you mind sharing your workflow somehow through screenshots or the like? I'm most interested how you:
- Go from reading PDFs to taking notes
- Go from taking notes to organizing and linking notes
- Find the right notes and use them when you need to write something