Obsidian for medicine/academics?

Knowledge management
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Hello everyone! I have found this community and software to be incredible, and I am so excited to have found this. I’ve been using Obsidian for a few months now and am starting to get the hang of it, but I would love to see if anybody is using Obsidian who is currently practicing medicine, or involved in an academic field. I find myself struggling to develop and organize a comprehensive system that is also accessible for time-sensitive clinical reference. I was just hoping we might use this thread to discuss best practices and learn something!

Thanks!

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Me too!
I’m a Psychologist, I’m not a researcher nor an academic, but I rely heavily on papers.
I’m eager to listen to the suggestions from other people.

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i’m Nutritionist and are moving lots of my Collection, which is growing over 20 Years with different Files and Software, over to Obsidian.
I do it simple, trying using speaking Note-Names and Links sometimes.
It seems to be very useful, after only a few Months filling in.

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I am also trying to transfer mine over, little by little. Wish I had a good system from the start, though!

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I’m a doctor rotating within internal medicine. I’m also experimenting with a system of my own, which has turned out to be a variation of the zettelkasten.

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@syncretizm what does your workflow look like?

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I use a variant of zettelkasten, which I call CSI:

  • Top level: Connectors
  • Middle level: Summaries
  • Bottom level: Inputs

Everything new to the system, including thoughts, things I learn, MCQs from online question banks, anki decks, ward rounds, teaching sessions, journal clubs, research papers, etc - each gets their own Input note. In zettelkasten this is similar to transient and literature notes, but I don’t separate them.

From these Inputs, I identify concepts and merge perspectives in Summary notes. For example, a note on [[renal artery stenosis]] would be classified as a #diagnosis but would contain a synthesis referencing many input notes from teachings, exams, question banks, textbooks, etc. This is akin to an immature Permanent Note or Evergreen Note.

I make it a point to go deeper into Connector Notes, where I identify themes of deeper connection or difference. For example, connecting the physiology of the body to a management principle. You can see it as a connector between summaries. In my opinion, this is what brings notetaking to the next level. This is the area where real, personal ideas are superimposed over mere collection.

So to recap, everything raw or coming from other people goes into the Input notes, subsequently distilled into Summary notes. These little summaries are then connected via Connector notes.

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Just an info about Inputs and Summaries: do you delete the Inputs when you create Summaries?
Or you just refer to Inputs from Summaries?

Nice workflow: I’m still having some struggle about citations and academic papers.
I’d like to create atomic notes from them, but I fear I lose the connection with the original paper and lose the ability to connect them when I come back in the Future.

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I never delete Inputs, because inputs contain dates, information, authors, etc. When sources get renewed/revised/updated, I create a new input note that contrasts the old note.

Summaries are basically like review articles, where ideas are synthesised. Except: it also follows the atomic principle, where I try to keep each summary as succinct as possible. They should act like nodes, or referenceable APIs.

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Very nice. I really like the idea of summary notes. Also, do you make separate notes for connector notes? I feel like my notes are just getting bloated, but I don’t necessarily want to make separate cards for the epidemiology, pathophysiology, presentation, diagnosis, and treatment for a specific condition.

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Connector notes are like systematic reviews or meta-analyses, to put a rough analogy. For example, it could be a PICO question that tries to find the optimal strategy for a subpopulation, etc.

Or an overarching theme that helps to summarise/compare/contrast approaches across different conditions (eg. Anticoagulation therapies discussing SAPT/DAPT, in stroke vs DVT vs ischaemic heart disease vs etc).

Each summary is an atomic unit of knowledge, and each connector is akin to a molecule of different combinations.

I didn’t mean separating epidemiology, pathophysio etc. These can be in a single card. It’s hard to explain because I heavily use the local graph view as well to explore my graph, but being able to see these atomic note titles can help to identify gaps and previously undiscovered similarities/differences that encourage higher level thinking.

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I’ve been looking for a post like this for some time now. I’m actually a medical student looking to use Obsidian for organizing my notes.

I’m so excited about the things that Obsidian and similar note-taking apps bring to the table. I am also looking to start a research project revolving around using tools such as Obsidian and Roam Research for medical education. These are relatively new note-taking apps that provide ways of connecting concepts to each other, allowing for easier discovery of related concepts when studying/reviewing information. This is especially helpful in fields with a vast amount of information, such as medicine.

I am hoping to pitch an idea to one of my medical school professors to use Obsidian and/or Roam Research in a topic covered in the medical curriculum (such as Pharmacology) and to gauge students’ reception to it.

On another note, I also recently encountered a great resource online called the Unified Medical Language System (UMLS) that seems amenable to being utilized in Obsidian if a markdown note for each medical concept mentioned in the UMLS is created. This would provide a standardized, nearly comprehensive reference to medical concepts (there are around 4 million+ concepts in the UMLS) to make use of in Obsidian. More specifically, this would require:

  1. Some way of transferring the concepts from the UMLS to obsidian markdown notes, perhaps through a python program. Anyone who has downloaded the UMLS onto their computer could potentially make use of such a program to automatically create concept notes which they can add to their individual vaults.
  2. A way of navigating around the sheer magnitude of notes that can potentially be created, as I worry that Obsidian may not be able to handle 4 million+ conceptual notes. Perhaps curating them in some way so as to only include those concepts that are relevant to a given Obsidian vault may be the best option.

I would be interested to hear from anyone who has thoughts on the above. If anyone is familiar with the UMLS or if anyone is interested in providing suggestions for how I can develop a research project around the use of Obsidian and other similar note-taking tools in the medical curriculum, please let me know.

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Man, that is an enormous project! I have never heard of the UMLS before, but it definitely intrigues me. The big thing I always think about for a research question is, what is the most specific question I can ask to help me accomplish my goal. For a proof of concept research question I would try to narrow in on something specific like MSK terms (my specialty, so clearly the best subject!) and focus on that. The big question is… what are we looking for as an outcome with this study?

The UMLS looks promising, but as a student it may be more beneficial to just work through First Aid and make those into notes/topics, and expand on them as needed. That would give you a great base of knowledge and would help with boards potentially.

I am still very much having lots of difficulties integrating my notes and findings, so I would love to hear if you are having success.

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I’m a family med physician, in the clinic full time. I’ve been using Obsidian for about 6 months and was using Ryder Carroll’s bullet journal system since 2018 before that. In the beginning, I basically did everything bullet journal style, but have slowly incorporated a more traditional zettelkasten approach. Keeping notes atomic has been key.

I still bullet journal:
Daily notes - my catch all. I put Fleeting notes in here, as well as my evening reflection. I use inline syntax like
Gratitude:: my new mouse is helping my carpal tunnel!
I also have yaml front matter that I use to monitor things like meds, hours slept, alcohol intake, etc.
Weekly/monthly notes - this is mostly dataview queries where I can visualize trends, review any open tasks, and read a summary of my logs. I have a gratitude log, a list of my daughters firsts, and funny things that happen at work.

Zettelkasten
Here’s where I keep things atomic. If I have no time to elaborate, I’ll write a thought down in my daily note using my zfleet:: shortcut. (ex. zfleet:: Andre 3000 and Rick Rubin podcast discuss social anxiety.) If I have time to elaborate, then I’ll make literature note. I make a conscious effort to prioritize writing it down. I’ve written paragraphs in my daily note before, then just cutting and pasting into a literature note later.

Literature notes - when there is an article or video that interests me, I write a literature note of why it struck a cord with me. I write it in my words as if I’m teaching it to myself 10 years later. (you bet your ass I have a lit note on the andre 3000/rick rubin podcast).
I also write lit notes on interesting case studies. Interesting presentations, side effects, cases where in stumped, etc I’ve seen in clinic.
I have “people” notes. I’m not sure where this fits. But if I hear Dr. X will see a patient for Y, then Dr. X will have their own note, basically like a rolodex. It’s helped a few times now. I had a 17yo who asked who in town they can talk to for a breast reduction, and I had a note saying Dr. X sees minors for breast reduction. It had all the necessary contact info, so I copied and pasted it into their after visit summary.

Permanent notes - this is the best part. These are my ideas that I’ve put together. There’s no end in sight. For example, from the rick rubin podcast, I’ve added onto my notes about social anxiety. I also created a new one about how Andre 3000’s creative rut stems from his fear of failure and tainting his legacy. This led to unexpected places like parenting advice (giving positive feedback regarding characteristics (so smar!) vs accomplishments (so hardworking!) ), and adhd management (when it’s ok to let your brain be unproductive on purpose).

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Hello Salamander23,

I am an anesthesiologist who has been in academics and now in private practice. I still have involvement with medication education and have thought about using Obsidian for education as you mention in your note and would be happy to correspond with you more on your ideas and even help you with this project. I have considered the development of vaults that could be specific for one specialty or medical school topic that could be used by both students and professors. There could be an ‘importing’ of sorts that with the proper design would allow for an emergent medical knowledge that grew and was customized by each student as they matriculated with their education. There is potential in something like as opposed to standard note taking applications. Reach out to me with a private message and I am happy to talk with you more.

As for the UMLS, you are correct, you could generate >4M notes using the taxonomies contained in the UMLS, however I am not sure this would lead to much in the way of utility. Taxonomies such as these are useful for coding and aggregation of data, but to have that many ‘empty’ notes would likely lead to slow processing without much utility on an individuals emerging knowledge. This being said, I do think using the terms contained (ie in a standardized fashion that this taxonomy maintains) could be useful for tagging or grouping the information you place into your own vault. Python would be able to do this, relatively easily, but again not sure it would help unless you had some specific goal you were shooting for?

Good luck and looking forward to hearing more on this thread

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Thanks @dmv6 and @jrennicke for your thoughtful replies. I’ve had a few more thoughts since my last post, so be prepared for a longer read. I hope it is beneficial.

Before I delve any further, I just want to clarify for anyone reading that my research project idea and my suggestion of incorporating the UMLS into Obsidian are two separate topics. I don’t think I will be making use of the UMLS in my research unless it’s useful for its development or if it can provide an additional angle to my research that makes sense. Or maybe incorporating the UMLS into Obsidian and gathering feedback can be another project on its own… it’s all theory at this point.

I will only be discussing the possibility of incorporating UMLS into Obsidian below, as a potential means of organizing biomedical notes in Obsidian (since that is the focus of this thread). Even if you aren’t interested in using the UMLS, some of the things mentioned can be helpful in terms of organizing notes by their types or relationships.

As for elaboration of my proposed research project idea, I will be corresponding privately with anyone interested, as I realize this thread may not the best place for it.

Possible Utility of the UMLS in Obsidian

  • Why try to incorporate conceptual data from the UMLS into Obsidian? Let’s start with this before moving to the cons.

    • It provides a shared language for people looking to share biomedical notes.
      • Let’s say you have your own vault that has UMLS concepts incorporated in it. A friend of yours also made a vault with incorporated UMLS concepts. When you share vaults, you now have a shared point of reference, especially if you’ve both placed your UMLS concept notes in a designated folder and are using the same naming scheme for those notes. After transferring your friend’s UMLS concept notes into your designated folder, and with some processing to remove duplicate concept notes, you can retain your own created links to a UMLS concept while also appreciating your friends links to that same topic.
    • It allows for aliases for any given concept.
      • All concepts in the UMLS come with a documented record of alternate names for that same concept, so aliases are built into the UMLS from the get-go. It’s just a matter of transferring them to a UMLS concept note in your vault. You are also free to personally add your own aliases, but at least you didn’t have to think about the ones that already come with the UMLS.
    • It can be useful for tagging/grouping information in a person’s own vault, as stated by @dmv6
      • How?
        • The UMLS contains a semantic network that categorizes concepts according to 127 different broad subject categories (i.e. semantic types) and at least 54 relationships (i.e. semantic relations/relationships). These can be utilized in Obsidian in the following ways:

          • Tagging UMLS concept notes with their semantic types. For example, the note [[Cough]] can be labeled as:

            #Sign_or_Symptom

            or can alternatively be assigned a nested tag, as follows:

            #Finding/Sign_or_Symptom

          • Making queryable relationships between concepts. Can be done by using the Dataview plugin and writing the semantic relationship as a custom field. For example, let’s say I have the note [[Staphylococcus]]. I can write the following to make a queryable relationship between [[Staphylococcus]] and two other notes: [[Gram-positive bacteria]] and [[Bacteria]], based on the UMLS Semantic Relationship isa:

            isa:: [[Gram-positive bacteria]], [[Bacteria]]

            or I can write this in the YAML header:

            ---
isa: ["[[Gram-positive bacteria]]", "[[Bacteria]]"]
---

            or

            ---
isa:
 - "[[Gram-positive bacteria]]"
 - "[[Bacteria]]"
---

          • Making relationships between concepts visible on a local graph view. Can be done using the Juggl plugin and writing the semantic relationship as a bullet point. The relationship then becomes visible on the Juggl local graph view. For the [[Staphylococcus]] example, that would be:

            - isa [[Gram-positive bacteria]]

            image

          • Making relationships BOTH queryable and visible on local graph view. This is possible if you have both the Dataview and Juggl plugins, but it requires some CSS at the time of this writing. I wrote some CSS demonstrating how this can be done in a separate post, although it does have the limitation that you can’t show more than one Dataview-style link between a pair of notes in Juggl at the same time. The creator of the Juggl plugin has mentioned that having this sort of typed link / inline dataview property hybrid is on the radar for Juggl plugin development, however.

  • Cons or obstacles to incorporating the UMLS into Obsidian:

    • Generating >4M notes from the UMLS would slow things down needlessly. This was one of my initial concerns and was also brought up by @dmv6.
    • Depending on your situation, trying to incorporate the UMLS into your Obsidian notes may not be the most beneficial. This is alluded to by @jrennicke when he wrote that for me as a medical student, it may be more beneficial to just use First Aid. That makes sense, since the vast majority of UMLS concepts are not exactly relevant to what I need to know for boards.

  • Possible solution to the cons/obstacles in incorporating the UMLS into Obsidian:

    • Perhaps a python program can be written that scans a person’s notes in their Obsidian vault, identifies mentioned UMLS concepts, and makes new notes for those concepts alone. Here’s an example of the steps such a program could potentially take:
      1. Use scispaCy for UMLS concept identification from your Obsidian notes:
        • scispaCy is a natural language processing library in python that identifies scientific/biomedical entities in free-form text and can identify related UMLS concepts. As of this writing, it uses the 2020AA version of the UMLS, and identifies category 0, 1, 2, and 9 concepts (the different categories correspond to different levels of allowed usage as specified by the UMLS License Agreement). Here is a demo. I’ve downloaded and tested out scispaCy, but I have yet to use it for my Obsidian notes.
      2. Create new markdown files for the UMLS concepts identified by scispaCy and link to those notes using Obsidian-style internal links.

I hope I’ve added more to the discussion. I hope that at least some of what I suggested can be practically implemented in a useful manner.

A large part of what I’ve written can only be put to maximal effect if there is a computer program that can automatically do the work of creating notes using UMLS concepts for you. If there is anyone who is willing to work with me in writing a python program that can accomplish this, I would really appreciate it.

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Hi @Salamander23,

Thank you so much for this post. I am now reading this and wondering if you or anyone have looked into integrating this recently.

At this time I am looking into integrating UMLS for the reasons above. I have installed dataview plugin and the rest API. Wondering if anyone can provide some guidance to navigate this.

Any insight/assistance is much appreciated!

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Wow, great thread. I’m an Emerg Physician and do stuff in Quality/Safety and teaching as well.

For time-sensitive reference, I’ve used the Obsidian URL’s (put it elsewhere) to click on it and get to the proper note. Searching on my phone while working can be a bit fiddly.

I try to keep my vault as simple as possible. I only create structure when I need it.

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