Newbie Help: Starting my 2nd brain. Migrating from OneNote with many files in OneDrive

Creating a knowledge database vault from scratch migrating from OneNote with a lot of files stored on OneDrive

Hello everybody and thanks for having me!

i am amazed by the things that are possible with obsidian but i feel a bit overwhelmed at the same time. Maybe i can get some input to help me sort out my issues. This will be a long post but i hope to describe my questions in enough detail to be able to get the help i seek.

Background: i am a veterinarian and i collected a large number of files over the years. PDFs, ebooks, videos, lecture notes, pictures, snippets of homepages. Some of the books are rather large PDF Files (several hundred MB, several hundred pages). Everything is on OneDrive in hierarchical folders. I linked every file in OneNote in order to access it from different paths (i.g. an article about parasites in sheep can be accessed via the sheep section AND the parasite section AND the diseases section).

Trying to do: i want to migrate my knowledge database to obsidian. i want to get off to a good start and plan in advance instead of migrating and indexing to then realize i should have proceeded differently. I have a decent structure in my folders but too many subfolders. I am considering to rework my folder structure first to follow the PARA or ACCESS principle.

Accessing the vault: I will need to access the database from pc, android tablet and android phone.

My most important questions are:

  1. Do you suggest to move all files into a single obsidian vault (70 gigabyte, mostly pdf)

OR should i keep them externally in one drive and rework my folder structure there for better accessibility (PARA, ACCESS,…)? If yes please help me to understand when i should embed them in a obsidian note and when i should only use a link to the file in OneDrive.

OR should i follow the suggestion i read in the forum to have one vault (A) for attachments only, one for notes only (B) and combined vault (C) to form links?
Regarding accessibility on my phone i am worried about the number and size of the many attachments.

  1. i am sometimes writing scientific papers. I have experience working with zotero and i am considering to update my library there first. Meaning that i will categorize all ebooks and pdfs there and then use the plugins to move the library to obsidian including metadata.

I am sorry if these questions seem trivial for some people. I got a lot of input how i could proceed in videos, articles and forum posts but i lack the experience in obsidian to make the right choice. I feel like i should make that choice before i actually start incorporating stuff in obsidian.

Plan on how to proceed right now - will be updated according to the input i receive: 1. update folder structure in OneDrive using PARA or ACCESS system. 2. update Zotero to include all input sources (books, scientific papers) and export Zotero library to Obsidian. 3. Start my vault by strategically moving data from OneNote to Obsidian using the imported files from Zotero

Things I have tried

I read a lot of topics in the forum regarding how to deal with many attachments and found a lot of different suggestions as i described above. I watch youtube videos by Zsolt and others regarding how to build knowledge databases. i read articles.

Regards and thank you for reading the whole post :slight_smile:

I am in a different profession (history), with a very similar position: large numbers and types of files, existing linked notes in different systems (including OneNote), extensive annotations and comments on PDFs and other documents, etc.

I would never consider the path you laid out @PR2ndbrain.

In the past, I attempted a massive data migration and restructuring of my documents and notes. It was ultimately fruitless because after a few weeks of aggressive migration of notes and rebuilding links, the project would take years, which would put me years behind the curve in focusing my time and energy on the research.

Second, it’s important to not jump into software like Obsidian, with the sometimes daunting variety of approaches. It’s better to start fresh, with the next new research and documentation effort that you have planned, and test out the system you think you want. I can almost guarantee that the approach with Obsidian you trial on day one is not where you’ll end in 30, 90, 180+ days. And, that’s just fine – experimentation and learning on the job are part of the beauty and challenge of using PKMs.

Third, I think it’s safe to assume that much of what you already have has worked well for you for a very long time. Otherwise you would have abandoned it. So, think about why you want to abandon it now by transferred the whole superstructure to a new environment. Because Obsidian is shiny and new and the cool kids tell you it’s wonderful? (Be careful listening to too many video experts.) Or, because Obsidian has features A to Z (list them for yourself) that would go far beyond your current and required or desired new faculties, with sound reasons for make the change to get the features, and a detailed plan to get there.

Fourth, Obsidian is terrific. For note making and linking. It’s not much good for document management. (Others here will likely say the opposite. Fine, this is my experience not someone elses’.) Keep your files in Zotero / OneDrive, and reference them in Obsidian as needed.

Finally, for better or worse (and I assume most often for the better), you’ve invested a huge chunk of your life in managing a knowledge base that you already have. Forget the "second brain cant; no such thing exists except as a marketing term. The reality is, we use the only brain we have and support it in whatever organization methods that help us learn and manage our interests and time. Even if what you have has, unfortunately, never worked for you, it’s never going to be a good thing, in my personal opinion, to try to move it all over to a new environment – especially if that environment is one you do not yet have deep personal experience using. It is never hard to get hands-on with Obisidan, but it is made really difficult if the first goal is not to “start and learn”, but to “pump and dump” knowledge base data from another system.

Good luck. Take small steps.


Hello Roy,

thank you very much for your in depth reply i didnt expect to get a reply that quickly and that detailed!

Your text got my thinking what i actually want to achieve. And it made me think about the effort i would have to put in to get the outcome that i am hoping for. Thank you for sharing a different view on my situation! I am looking forward to what other people might share but i realized with your reply already that moving the whole stuff is really a bad idea. That saved me a lot of work regardless on how i will proceed from here.

Have a nice weekend

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Roy’s answer is excellent. I also fought with the management of information from the 1997 when I started with Clipper database, Foxpro, Winhelp (hlp - this one I loved so much), Microsoft Compiled HTML Help (chm), Cintanotes, Onenote, Evernote, Zotero, Thebrain, Simplenote, Microsoft Office, Google Drive, Keep, Piggydb, DTsearch, Alltags, Tagging for Windows, File meta, Typora, Logseq, Obsidian, Xmind, Citavi, Tropy, TiddlyWiki, localhost Wordpress, Aeon Timeline, Calibre, Dynalist, Workflowy, Cherrytree, Tagspaces, help systems, saving data to jpg, pdf, use OCR systems, file organizing tools, Copernic Desktop Search, and so many other software and ways to organize, index, tag, visualize my information of text, video, audio, PDF and other formats. Some apps have many useful features to link information, annotate text and images in PDFs, save, convert, index, search data efficiently, manage, display, filter images and other files, most of these will have problems with very large amount of information. I waited features to appear in beloved apps that never appeared, some apps development halted, many became unusable with Gbytes of info, some had ugly UI or had lack of important features even it were attractive. So because of it I have tons of data in Zotero, Cintanotes, Onenote, Evernote, Thebrain I intended to move but requires so much time I would need just doing data moving and organization more than 1 year or more. After that I found I have 30k files in it. After all I love the linking of information in Thebrain, the beauty and features of Evernote and Onenote, the unique features of Zotero, the way Obsidian and Logseq can manage markdown and annotate PDFs, the way can filter and preview data. So, trying to preserve information for long term archiving (ex. SingleFile html, PDF portolios, zip, pdf, etc.), tagging and organizing in folders to find all quickly, creating various formats to adapt in multiple apps required so much time. I have more data unorganized and very large number of bookmarks saved and exported in files. Some people use multiple apps to organize information, I liked (theoretically) the way to use a single one and searched the one that have most of features, UI and speed. And was hard. I also tried to organize files in folders and index all with file indexing and searching tool. There are so many ways none are perfect. Lost so many time organizing. Know persons who use just bookmarks or don’t organize just put all the info in a few main folders.
Cloud search an AI are also great. Cloud space is expensive when you need more.
I am attracted to clean the save information but requires much time, copy paste, delete, tagging, linking. Later I save information with SingleFile as html put in, drag full sized images from articles in the same subfolder and create a thumbnailed bookmark also. I still love many note management software, the way it work and display data. But don’t have time to just organize. The time is required for reading. So not very important information is just saved as html and bookmarked and the next is followed. Requires 1 minute. To copy paste, clean, format, tag, link an article requires much more time, to put in a software that locks the information that later reqs years to export and reorganize is so hard. Most of the tried apps became unusable after a time, because of the number of information, files, images, video, audio attachments I put in. Then the migration started. And after a time a realized the new software can’t support one or more features the previous could handle so well. And I was looked for more than that.
I love information to be in one place, organized, searchable, text with images, videos, audio, scanned papers OCRed, annotated such as PDFs, the usage of mathematical, chemical formulas, graphs, in a possible fastest way. A wish, a dream which is partially satisfied by some apps.
I think the simplest way (for me putting all information in a big container with folders) is great even not perfect but requires less time and more time remains for reading (till I find a better solution ;)).


Hello stefan44,

i was on holidays for a week but was delighted to come back to another great response. It feels liberating to have other people dealing with the same issues and insecurities when organizing the data. My PKM has been very helpful in my work and my personal development but it certainly is a lot of work maintaining it.
The most important learnings i had in the responses to my questions:

Dont stress using different softwares its ok.

Keep your folders if you like them.

Focus on reading and dont waste all the time organizing.

And lastly this is a great forum with helpful and insightful members.

Thank you!

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