How to Use Obsidian to Boost Research Productivity
Tools for managing your PhD projects, reading lists, notes, and inspiration.
As a researcher, you have to know everything. But knowledge is useless if it cannot be accessed quickly. An easy-to-use method of archiving information makes taking notes effortless and enjoyable.
As a PhD student in Artificial Intelligence, I use Obsidian (https://obsidian.md) to manage my knowledge.
The article has three parts:
- What is a note, how to organize notes, tags, folders, and links? This section is tool-agnostic, so you can use most of these ideas with any note-taking app.
- Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
- Workflows: How to use Zotero to take notes from papers, manage multiple projects' notes, create MOCs with Dataview, and more. This section explains how to use Obsidian to solve common scientific problems and manage/maintain your knowledge effectively.
This list is not perfect or complete, but it is my current solution to problems I've encountered during my PhD. Please leave additional comments or contact me if you have any feedback. I'll try to update this article.
Throughout the article, I'll refer to your digital library as your "Obsidian Vault" or "Zettelkasten".
Other useful resources are listed at the end of the article.
1. Philosophy: Taking and organizing notes
Carl Sagan: “To make an apple pie from scratch, you must first create the universe.”
Before diving into Obsidian, let's establish a Personal Knowledge Management System and a Zettelkasten. You can skip to Section 2 if you already know these terms.
Niklas Luhmann, a prolific sociologist who wrote 400 papers and 70 books, inspired this section and much of Zettelkasten. Zettelkasten means “slip box” (or library in this article). His Zettlekasten had around 90000 physical notes, which can be found here.
There are now many tools available to help with this process. Obsidian's website has a good introduction section: https://publish.obsidian.md/hub/
Notes
We'll start with "What is a note?" Although it may seem trivial, the answer depends on the topic or your note-taking style. The idea is that a note is as “atomic” (i.e. You should read the note and get the idea right away.
The resolution of your notes depends on their detail. Deep Learning, for example, could be a general description of Neural Networks, with a few notes on the various architectures (eg. Recurrent Neural Networks, Convolutional Neural Networks etc..).
Limiting length and detail is a good rule of thumb. If you need more detail in a specific section of this note, break it up into smaller notes. Deep Learning now has three notes:
- Deep Learning
- Recurrent Neural Networks
- Convolutional Neural Networks
Repeat this step as needed until you achieve the desired granularity. You might want to put these notes in a “Neural Networks” folder because they are all about the same thing. But there's a better way:
#Tags and [[Links]] over /Folders/
The main issue with folders is that they are not flexible and assume that all notes in the folder belong to a single category. This makes it difficult to make connections between topics.
Deep Learning has been used to predict protein structure (AlphaFold) and classify images (ImageNet). Imagine a folder structure like this:
- /Proteins/
- Protein Folding
- /Deep Learning/
- /Proteins/
Your notes about Protein Folding and Convolutional Neural Networks will be separate, and you won't be able to find them in the same folder.
This can be solved in several ways. The most common one is to use tags rather than folders. A note can be grouped with multiple topics this way. Obsidian tags can also be nested (have subtags).
You can also link two notes together. You can build your “Knowledge Graph” in Obsidian and other note-taking apps like Obsidian.
My Knowledge Graph. Green: Biology, Red: Machine Learning, Yellow: Autoencoders, Blue: Graphs, Brown: Tags.
My Knowledge Graph and the note “Backrpropagation” and its links.
Backpropagation note and all its links
Why use Folders?
Folders help organize your vault as it grows. The main suggestion is to have few folders that "weakly" collect groups of notes or better yet, notes from different sources.
Among my Zettelkasten folders are:
My Zettelkasten's 5 folders
They usually gather data from various sources:
MOC: Map of Contents for the Zettelkasten.
Projects: Contains one note for each side-project of my PhD where I log my progress and ideas. Notes are linked to these.
Bio and ML: These two are the main content of my Zettelkasten and could theoretically be combined.
Papers: All my scientific paper notes go here. A bibliography links the notes. Zotero .bib file
Books: I make a note for each book I read, which I then split into multiple notes.
Keeping images separate from other files can help keep your main folders clean.
I will elaborate on these in the Workflow Section.
My general recommendation is to use tags and links instead of folders.
Maps of Content (MOC)
Making Tables of Contents is a good solution (MOCs).
These are notes that "signposts" your Zettelkasten library, directing you to the right type of notes. It can link to other notes based on common tags. This is usually done with a title, then your notes related to that title. As an example:
An example of a Machine Learning MOC generated with Dataview.
As shown above, my Machine Learning MOC begins with the basics. Then it's on to Variational Auto-Encoders. Not only does this save time, but it also saves scrolling through the tag search section.
So I keep MOCs at the top of my library so I can quickly find information and see my library. These MOCs are generated automatically using an Obsidian Plugin called Dataview (https://github.com/blacksmithgu/obsidian-dataview).
Ideally, MOCs could be expanded to include more information about the notes, their status, and what's left to do. In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
2. Tools: Knowing Obsidian
Obsidian is my preferred tool because it is free, all notes are stored in Markdown format, and each panel can be dragged and dropped. You can get it here: https://obsidian.md/
Obsidian interface.
Obsidian is highly customizable, so here is my preferred interface:
The theme is customized from https://github.com/colineckert/obsidian-things
Alternatively, each panel can be collapsed, moved, or removed as desired. To open a panel later, click on the vertical "..." (bottom left of the note panel).
My interface is organized as follows:
How my Obsidian Interface is organized.
Folders/Search:
This is where I keep all relevant folders. I usually use the MOC note to navigate, but sometimes I use the search button to find a note.
Tags:
I use nested tags and look into each one to find specific notes to link.
cMenu:
Easy-to-use menu plugin cMenu (https://github.com/chetachiezikeuzor/cMenu-Plugin)
Global Graph:
The global graph shows all your notes (linked and unlinked). Linked notes will appear closer together. Zoom in to read each note's title. It's a bit overwhelming at first, but as your library grows, you get used to the positions and start thinking of new connections between notes.
Local Graph:
Your current note will be shown in relation to other linked notes in your library. When needed, you can quickly jump to another link and back to the current note.
Links:
Finally, an outline panel and the plugin Obsidian Power Search (https://github.com/aviral-batra/obsidian-power-search) allow me to search my vault by highlighting text.
Start using the tool and worry about panel positioning later. I encourage you to find the best use-case for your library.
Plugins
An additional benefit of using Obsidian is the large plugin library. I use several (Calendar, Citations, Dataview, Templater, Admonition):
Obsidian Calendar Plugin: https://github.com/liamcain
It organizes your notes on a calendar. This is ideal for meeting notes or keeping a journal.
Calendar addon from hans/obsidian-citation-plugin
Obsidian Citation Plugin: https://github.com/hans/
Allows you to cite papers from a.bib file. You can also customize your notes (eg. Title, Authors, Abstract etc..)
Plugin citation from hans/obsidian-citation-plugin
Obsidian Dataview: https://github.com/blacksmithgu/
A powerful plugin that allows you to query your library as a database and generate content automatically. See the MOC section for an example.
Allows you to create notes with specific templates like dates, tags, and headings.
Templater. Obsidian Admonition: https://github.com/valentine195/obsidian-admonition
Blocks allow you to organize your notes.
Plugin warning. Obsidian Admonition (valentine195)
There are many more, but this list should get you started.
3. Workflows: Cool stuff
Here are a few of my workflows for using obsidian for scientific research. This is a list of resources I've found useful for my use-cases. I'll outline and describe them briefly so you can skim them quickly.
3.1 Using Templates to Structure Notes
3.2 Free Note Syncing (Laptop, Phone, Tablet)
3.3 Zotero/Mendeley/JabRef -> Obsidian — Managing Reading Lists
3.4 Projects and Lab Books
3.5 Private Encrypted Diary
3.1 Using Templates to Structure Notes
Plugins: Templater and Dataview (optional).
To take effective notes, you must first make adding new notes as easy as possible. Templates can save you time and give your notes a consistent structure. As an example:
An example of a note using a template.
### [[YOUR MOC]]
# Note Title of your note
**Tags**::
**Links**::
The top line links to your knowledge base's Map of Content (MOC) (see previous sections). After the title, I add tags (and a link between the note and the tag) and links to related notes.
To quickly identify all notes that need to be expanded, I add the tag “#todo”. In the “TODO:” section, I list the tasks within the note.
The rest are notes on the topic.
Templater can help you create these templates. For new books, I use the following template:
### [[Books MOC]]
# Title
**Author**::
**Date::
**Tags::
**Links::
A book template example.
Using a simple query, I can hook Dataview to it.
dataview
table author as Author, date as “Date Finished”, tags as “Tags”, grade as “Grade”
from “4. Books”
SORT grade DESCENDING
using Dataview to query templates.
3.2 Free Note Syncing (Laptop, Phone, Tablet)
No plugins used.
One of my favorite features of Obsidian is the library's self-contained and portable format. Your folder contains everything (plugins included).
Ordinary folders and documents are available as well. There is also a “.obsidian” folder. This contains all your plugins and settings, so you can use it on other devices.
So you can use Google Drive, iCloud, or Dropbox for free as long as you sync your folder (note: your folder should be in your Cloud Folder).
For my iOS and macOS work, I prefer iCloud. You can also use the paid service Obsidian Sync.
3.3 Obsidian — Managing Reading Lists and Notes in Zotero/Mendeley/JabRef
Plugins: Quotes (required).
3.3 Zotero/Mendeley/JabRef -> Obsidian — Taking Notes and Managing Reading Lists of Scientific Papers
My preferred reference manager is Zotero, but this workflow should work with any reference manager that produces a .bib file. This file is exported to my cloud folder so I can access it from any platform.
My Zotero library is tagged as follows:
My reference manager's tags
For readings, I usually search for the tags “!!!” and “To-Read” and select a paper. Annotate the paper next (either on PDF using GoodNotes or on physical paper).
Then I make a paper page using a template in the Citations plugin settings:
An example of my citations template.
Create a new note, open the command list with CMD/CTRL + P, and find the Citations “Insert literature note content in the current pane” to see this lovely view.
Citation generated by the article https://doi.org/10.1101/2022.01.24.22269144
You can then convert your notes to digital. I found that transcribing helped me retain information better.
3.4 Projects and Lab Books
Plugins: Tweaker (required).
PhD students offering advice on thesis writing are common (read as regret). I started asking them what they would have done differently or earlier.
“Deep stuff Leo,” one person said. So my main issue is basic organization, losing track of my tasks and the reasons for them.
As a result, I'd go on other experiments that didn't make sense, and have to reverse engineer my logic for thesis writing. - PhD student now wise Postdoc
Time management requires planning. Keeping track of multiple projects and lab books is difficult during a PhD. How I deal with it:
- One folder for all my projects
- One file for each project
I use a template to create each project
### [[Projects MOC]]
# <% tp.file.title %>
**Tags**::
**Links**::
**URL**::
**Project Description**::## Notes:
### <% tp.file.last_modified_date(“dddd Do MMMM YYYY”) %>
#### Done:
#### TODO:
#### Notes
You can insert a template into a new note with CMD + P and looking for the Templater option.
I then keep adding new days with another template:
### <% tp.file.last_modified_date("dddd Do MMMM YYYY") %>
#### Done:
#### TODO:
#### Notes:
This way you can keep adding days to your project and update with reasonings and things you still have to do and have done. An example below:
Example of project note with timestamped notes.
3.5 Private Encrypted Diary
This is one of my favorite Obsidian uses.
Mini Diary's interface has long frustrated me. After the author archived the project, I looked for a replacement. I had two demands:
- It had to be private, and nobody had to be able to read the entries.
- Cloud syncing was required for editing on multiple devices.
Then I learned about encrypting the Obsidian folder. Then decrypt and open the folder with Obsidian. Sync the folder as usual.
Use CryptoMator (https://cryptomator.org/). Create an encrypted folder in Cryptomator for your Obsidian vault, set a password, and let it do the rest.
If you need a step-by-step video guide, here it is:
Conclusion
So, I hope this was helpful!
In the first section of the article, we discussed notes and note-taking techniques. We discussed when to use tags and links over folders and when to break up larger notes.
Then we learned about Obsidian, its interface, and some useful plugins like Citations for citing papers and Templater for creating note templates.
Finally, we discussed workflows and how to use Zotero to take notes from scientific papers, as well as managing Lab Books and Private Encrypted Diaries.
Thanks for reading and commenting :)
Read original post here
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Inventories by Concept
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Low numbers.
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How often do you forget an article or book's key point? Have you ever wasted hours looking for a saved file?
If so, you're not alone. Information overload affects millions of individuals worldwide. Information overload drains mental resources and causes anxiety.
This is when the second brain comes in.
Building a second brain doesn't involve duplicating the human brain. Building a system that captures, organizes, retrieves, and archives ideas and thoughts. The second brain improves memory, organization, and recall.
Digital tools are preferable to analog for building a second brain.
Digital tools are portable and accessible. Due to these benefits, we'll focus on digital second-brain building.
Brainware
Digital Brains are external hard drives. It stores, organizes, and retrieves. This means improving your memory won't be difficult.
Memory has three components in computing:
Recording — storing the information
Organization — archiving it in a logical manner
Recall — retrieving it again when you need it
For example:
Due to rigorous security settings, many websites need you to create complicated passwords with special characters.
You must now memorize (Record), organize (Organize), and input this new password the next time you check in (Recall).
Even in this simple example, there are many pieces to remember. We can't recognize this new password with our usual patterns. If we don't use the password every day, we'll forget it. You'll type the wrong password when you try to remember it.
It's common. Is it because the information is complicated? Nope. Passwords are basically letters, numbers, and symbols.
It happens because our brains aren't meant to memorize these. Digital Brains can do heavy lifting.
Why You Need a Digital Brain
Dual minds are best. Birth brain is limited.
The cerebral cortex has 125 trillion synapses, according to a Stanford Study. The human brain can hold 2.5 million terabytes of digital data. [2]
Building a second brain improves learning and memory.
Learn and store information effectively
Faster information recall
Organize information to see connections and patterns
Build a Digital Brain to learn more and reach your goals faster. Building a second brain requires time and work, but you'll have more time for vital undertakings.
Why you need a Digital Brain:
1. Use Brainpower Effectively
Your brain has boundaries, like any organ. This is true while solving a complex question or activity. If you can't focus on a work project, you won't finish it on time.
Second brain reduces distractions. A robust structure helps you handle complicated challenges quickly and stay on track. Without distractions, it's easy to focus on vital activities.
2. Staying Organized
Professional and personal duties must be balanced. With so much to do, it's easy to neglect crucial duties. This is especially true for skill-building. Digital Brain will keep you organized and stress-free.
Life success requires action. Organized people get things done. Organizing your information will give you time for crucial tasks.
You'll finish projects faster with good materials and methods. As you succeed, you'll gain creative confidence. You can then tackle greater jobs.
3. Creativity Process
Creativity drives today's world. Creativity is mysterious and surprising for millions worldwide. Immersing yourself in others' associations, triggers, thoughts, and ideas can generate inspiration and creativity.
Building a second brain is crucial to establishing your creative process and building habits that will help you reach your goals. Creativity doesn't require perfection or overthinking.
4. Transforming Your Knowledge Into Opportunities
This is the age of entrepreneurship. Today, you can publish online, build an audience, and make money.
Whether it's a business or hobby, you'll have several job alternatives. Knowledge can boost your economy with ideas and insights.
5. Improving Thinking and Uncovering Connections
Modern career success depends on how you think. Instead of overthinking or perfecting, collect the best images, stories, metaphors, anecdotes, and observations.
This will increase your creativity and reveal connections. Increasing your imagination can help you achieve your goals, according to research. [3]
Your ability to recognize trends will help you stay ahead of the pack.
6. Credibility for a New Job or Business
Your main asset is experience-based expertise. Others won't be able to learn without your help. Technology makes knowledge tangible.
This lets you use your time as you choose while helping others. Changing professions or establishing a new business become learning opportunities when you have a Digital Brain.
7. Using Learning Resources
Millions of people use internet learning materials to improve their lives. Online resources abound. These include books, forums, podcasts, articles, and webinars.
These resources are mostly free or inexpensive. Organizing your knowledge can save you time and money. Building a Digital Brain helps you learn faster. You'll make rapid progress by enjoying learning.
How does a second brain feel?
Digital Brain has helped me arrange my job and family life for years.
No need to remember 1001 passwords. I never forget anything on my wife's grocery lists. Never miss a meeting. I can access essential information and papers anytime, anywhere.
Delegating memory to a second brain reduces tension and anxiety because you'll know what to do with every piece of information.
No information will be forgotten, boosting your confidence. Better manage your fears and concerns by writing them down and establishing a strategy. You'll understand the plethora of daily information and have a clear head.
How to Develop Your Digital Brain (Your Second Brain)
It's cheap but requires work.
Digital Brain development requires:
Recording — storing the information
Organization — archiving it in a logical manner
Recall — retrieving it again when you need it
1. Decide what information matters before recording.
To succeed in today's environment, you must manage massive amounts of data. Articles, books, webinars, podcasts, emails, and texts provide value. Remembering everything is impossible and overwhelming.
What information do you need to achieve your goals?
You must consolidate ideas and create a strategy to reach your aims. Your biological brain can imagine and create with a Digital Brain.
2. Use the Right Tool
We usually record information without any preparation - we brainstorm in a word processor, email ourselves a message, or take notes while reading.
This information isn't used. You must store information in a central location.
Different information needs different instruments.
Evernote is a top note-taking program. Audio clips, Slack chats, PDFs, text notes, photos, scanned handwritten pages, emails, and webpages can be added.
Pocket is a great software for saving and organizing content. Images, videos, and text can be sorted. Web-optimized design
Calendar apps help you manage your time and enhance your productivity by reminding you of your most important tasks. Calendar apps flourish. The best calendar apps are easy to use, have many features, and work across devices. These calendars include Google, Apple, and Outlook.
To-do list/checklist apps are useful for managing tasks. Easy-to-use, versatility, budget, and cross-platform compatibility are important when picking to-do list apps. Google Keep, Google Tasks, and Apple Notes are good to-do apps.
3. Organize data for easy retrieval
How should you organize collected data?
When you collect and organize data, you'll see connections. An article about networking can assist you comprehend web marketing. Saved business cards can help you find new clients.
Choosing the correct tools helps organize data. Here are some tools selection criteria:
Can the tool sync across devices?
Personal or team?
Has a search function for easy information retrieval?
Does it provide easy data categorization?
Can users create lists or collections?
Does it offer easy idea-information connections?
Does it mind map and visually organize thoughts?
Conclusion
Building a Digital Brain (second brain) helps us save information, think creatively, and implement ideas. Your second brain is a biological extension. It prevents amnesia, allowing you to tackle bigger creative difficulties.
People who love learning often consume information without using it. Every day, they postpone life-improving experiences until they're forgotten. Useful information becomes strength.
Reference
[1] ^ Scientific American: What Is the Memory Capacity of the Human Brain?
[2] ^ Clinical Neurology Specialists: What is the Memory Capacity of a Human Brain?
[3] ^ National Library of Medicine: Imagining Success: Multiple Achievement Goals and the Effectiveness of Imagery
The Velocipede
2 years ago
Stolen wallet
How a misplaced item may change your outlook
Losing your wallet means life stops. Money vanishes. No credit. Your identity is unverifiable. As you check your pockets for the missing object, you can't drive. You can't borrow a library book.
Last seen? intuitively. Every kid asks this, including yours. However, you know where you lost it: On the Providence River cycling trail. While pedaling vigorously, the wallet dropped out of your back pocket and onto the pavement.
A woman you know—your son's art teacher—says it will be returned. Faith.
You want that faith. Losing a wallet is all-consuming. You must presume it has been stolen and is being used to buy every diamond and non-fungible token on the market. Your identity may have been used to open bank accounts and fake passports. Because he used your license address, a ski mask-wearing man may be driving slowly past your house.
As you delete yourself by canceling cards, these images run through your head. You wait in limbo for replacements. Digital text on the DMV website promises your new license will come within 60 days and be approved by local and state law enforcement. In the following two months, your only defense is a screenshot.
Your wallet was ordinary. A worn, overstuffed leather rectangle. You understand how tenuous your existence has always been since you've never lost a wallet. You barely breathe without your documents.
Ironically, you wore a wallet-belt chain. You adored being a 1993 slacker for 15 years. Your wife just convinced you last year that your office job wasn't professional. You nodded and hid the chain.
Never lost your wallet. Until now.
Angry. Feeling stupid. How could you drop something vital? Why? Is the world cruel? No more dumb luck. You're always one pedal-stroke from death.
Then you get a call: We have your wallet.
Local post office, not cops.
The clerk said someone returned it. Due to trying to identify you, it's a chaos. It has your cards but no cash.
Your automobile screeches down the highway. You yell at the windshield, amazed. Submitted. Art teacher was right. Have some trust.
You thank the postmaster. You ramble through the story. The clerk doesn't know the customer, simply a neighborhood Good Samaritan. You wish you could thank that person for lifting your spirits.
You get home, beaming with gratitude. You thumb through your wallet, amazed that it’s all intact. Then you dig out your chain and reattach it.
Because even faith could use a little help.