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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We're currently attempting to find equilibrium between opposites. It's superficial to defend extremes by stating we're only human or wired this way because both imply we have no control.
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In Google's own words:
A canonical URL is the page Google thinks is most representative of duplicate pages on your site.
— Google Search Console Help
You can indicate your preferred canonical URL. For various reasons, Google may choose a different page than you.
When set correctly, the canonical URL is usually your specified URL.
Canonical URLs determine which page will be shown in search results (unless a duplicate is explicitly better for a user, like a mobile version).
Canonical URLs can be on different domains.
Other ways to specify canonical URLs
Canonical tags are the most common way to specify a canonical URL.
You can also set canonicals by:
Setting the HTTP header rel=canonical.
All pages listed in a sitemap are suggested as canonicals, but Google decides which pages are duplicates.
Redirects 301.
Google recommends these methods, but they aren't all appropriate for every situation, as we'll see below. Each has its own recommended uses.
Setting canonical URLs isn't required; if you don't, Google will use other signals to determine the best page version.
To control how your site appears in search engines and to avoid duplicate content issues, you should use canonicalization effectively.
Why Duplicate Content Exists
Before we discuss why you should use canonical URLs and how to specify them in popular CMSs, we must first explain why duplicate content exists. Nobody intentionally duplicates website content.
Content management systems create multiple URLs when you launch a page, have indexable versions of your site, or use dynamic URLs.
Assume the following URLs display the same content to a user:
A search engine sees eight duplicate pages, not one.
URLs #1 and #2: the CMS saves product URLs with and without the category name.
#3, #4, and #5 result from the site being accessible via HTTP, HTTPS, www, and non-www.
#6 is a subdomain mobile-friendly URL.
URL #7 lacks URL #2's trailing slash.
URL #8 uses a capital "A" instead of a lowercase one.
Duplicate content may also exist in URLs like:
https://www.website.com
https://www.website.com/index.php
Duplicate content is easy to create.
Canonical URLs help search engines identify different page variations as a single URL on many sites.
SEO Canonical URLs
Canonical URLs help you manage duplicate content that could affect site performance.
Canonical URLs are a technical SEO focus area for many reasons.
Specify URL for search results
When you set a canonical URL, you tell Google which page version to display.
Which would you click?
https://www.domain.com/page-1/
https://www.domain.com/index.php?id=2
First, probably.
Canonicals tell search engines which URL to rank.
Consolidate link signals on similar pages
When you have duplicate or nearly identical pages on your site, the URLs may get external links.
Canonical URLs consolidate multiple pages' link signals into a single URL.
This helps your site rank because signals from multiple URLs are consolidated into one.
Syndication management
Content is often syndicated to reach new audiences.
Canonical URLs consolidate ranking signals to prevent duplicate pages from ranking and ensure the original content ranks.
Avoid Googlebot duplicate page crawling
Canonical URLs ensure that Googlebot crawls your new pages rather than duplicated versions of the same one across mobile and desktop versions, for example.
Crawl budgets aren't an issue for most sites unless they have 100,000+ pages.
How to Correctly Implement the rel=canonical Tag
Using the header tag rel="canonical" is the most common way to specify canonical URLs.
Adding tags and HTML code may seem daunting if you're not a developer, but most CMS platforms allow canonicals out-of-the-box.
These URLs each have one product.
How to Correctly Implement a rel="canonical" HTTP Header
A rel="canonical" HTTP header can replace canonical tags.
This is how to implement a canonical URL for PDFs or non-HTML documents.
You can specify a canonical URL in your site's.htaccess file using the code below.
<Files "file-to-canonicalize.pdf"> Header add Link "< http://www.website.com/canonical-page/>; rel=\"canonical\"" </Files>301 redirects for canonical URLs
Google says 301 redirects can specify canonical URLs.
Only the canonical URL will exist if you use 301 redirects. This will redirect duplicates.
This is the best way to fix duplicate content across:
HTTPS and HTTP
Non-WWW and WWW
Trailing-Slash and Non-Trailing Slash URLs
On a single page, you should use canonical tags unless you can confidently delete and redirect the page.
Sitemaps' canonical URLs
Google assumes sitemap URLs are canonical, so don't include non-canonical URLs.
This does not guarantee canonical URLs, but is a best practice for sitemaps.
Best-practice Canonical Tag
Once you understand a few simple best practices for canonical tags, spotting and cleaning up duplicate content becomes much easier.
Always include:
One canonical URL per page
If you specify multiple canonical URLs per page, they will likely be ignored.
Correct Domain Protocol
If your site uses HTTPS, use this as the canonical URL. It's easy to reference the wrong protocol, so check for it to catch it early.
Trailing slash or non-trailing slash URLs
Be sure to include trailing slashes in your canonical URL if your site uses them.
Specify URLs other than WWW
Search engines see non-WWW and WWW URLs as duplicate pages, so use the correct one.
Absolute URLs
To ensure proper interpretation, canonical tags should use absolute URLs.
So use:
<link rel="canonical" href="https://www.website.com/page-a/" />And not:
<link rel="canonical" href="/page-a/" />If not canonicalizing, use self-referential canonical URLs.
When a page isn't canonicalizing to another URL, use self-referencing canonical URLs.
Canonical tags refer to themselves here.
Common Canonical Tags Mistakes
Here are some common canonical tag mistakes.
301 Canonicalization
Set the canonical URL as the redirect target, not a redirected URL.
Incorrect Domain Canonicalization
If your site uses HTTPS, don't set canonical URLs to HTTP.
Irrelevant Canonicalization
Canonicalize URLs to duplicate or near-identical content only.
SEOs sometimes try to pass link signals via canonical tags from unrelated content to increase rank. This isn't how canonicalization should be used and should be avoided.
Multiple Canonical URLs
Only use one canonical tag or URL per page; otherwise, they may all be ignored.
When overriding defaults in some CMSs, you may accidentally include two canonical tags in your page's <head>.
Pagination vs. Canonicalization
Incorrect pagination can cause duplicate content. Canonicalizing URLs to the first page isn't always the best solution.
Canonicalize to a 'view all' page.
How to Audit Canonical Tags (and Fix Issues)
Audit your site's canonical tags to find canonicalization issues.
SEMrush Site Audit can help. You'll find canonical tag checks in your website's site audit report.
Let's examine these issues and their solutions.
No Canonical Tag on AMP
Site Audit will flag AMP pages without canonical tags.
Canonicalization between AMP and non-AMP pages is important.
Add a rel="canonical" tag to each AMP page's head>.
No HTTPS redirect or canonical from HTTP homepage
Duplicate content issues will be flagged in the Site Audit if your site is accessible via HTTPS and HTTP.
You can fix this by 301 redirecting or adding a canonical tag to HTTP pages that references HTTPS.
Broken canonical links
Broken canonical links won't be considered canonical URLs.
This error could mean your canonical links point to non-existent pages, complicating crawling and indexing.
Update broken canonical links to the correct URLs.
Multiple canonical URLs
This error occurs when a page has multiple canonical URLs.
Remove duplicate tags and leave one.
Canonicalization is a key SEO concept, and using it incorrectly can hurt your site's performance.
Once you understand how it works, what it does, and how to find and fix issues, you can use it effectively to remove duplicate content from your site.
Canonicalization SEO Myths
The woman
2 years ago
The best lesson from Sundar Pichai is that success and stress don't mix.
His regular regimen teaches stress management.
In 1995, an Indian graduate visited the US. He obtained a scholarship to Stanford after graduating from IIT with a silver medal. First flight. His ticket cost a year's income. His head was full.
Pichai Sundararajan is his full name. He became Google's CEO and a world leader. Mr. Pichai transformed technology and inspired millions to dream big.
This article reveals his daily schedule.
Mornings
While many of us dread Mondays, Mr. Pichai uses the day to contemplate.
A typical Indian morning. He awakens between 6:30 and 7 a.m. He avoids working out in the mornings.
Mr. Pichai oversees the internet, but he reads a real newspaper every morning.
Pichai mentioned that he usually enjoys a quiet breakfast during which he reads the news to get a good sense of what’s happening in the world. Pichai often has an omelet for breakfast and reads while doing so. The native of Chennai, India, continues to enjoy his daily cup of tea, which he describes as being “very English.”
Pichai starts his day. BuzzFeed's Mat Honan called the CEO Banana Republic dad.
Overthinking in the morning is a bad idea. It's crucial to clear our brains and give ourselves time in the morning before we hit traffic.
Mr. Pichai's morning ritual shows how to stay calm. Wharton Business School found that those who start the day calmly tend to stay that way. It's worth doing regularly.
And he didn't forget his roots.
Afternoons
He has a busy work schedule, as you can imagine. Running one of the world's largest firm takes time, energy, and effort. He prioritizes his work. Monitoring corporate performance and guaranteeing worker efficiency.
Sundar Pichai spends 7-8 hours a day to improve Google. He's noted for changing the company's culture. He wants to boost employee job satisfaction and performance.
His work won him recognition within the company.
Pichai received a 96% approval rating from Glassdoor users in 2017.
Mr. Pichai stresses work satisfaction. Each day is a new canvas for him to find ways to enrich people's job and personal lives.
His work offers countless lessons. According to several profiles and press sources, the Google CEO is a savvy negotiator. Mr. Pichai's success came from his strong personality, work ethic, discipline, simplicity, and hard labor.
Evenings
His evenings are spent with family after a busy day. Sundar Pichai's professional and personal lives are balanced. Sundar Pichai is a night owl who re-energizes about 9 p.m.
However, he claims to be most productive after 10 p.m., and he thinks doing a lot of work at that time is really useful. But he ensures he sleeps for around 7–8 hours every day. He enjoys long walks with his dog and enjoys watching NSDR on YouTube. It helps him in relaxing and sleep better.
His regular routine teaches us what? Work wisely, not hard, discipline, vision, etc. His stress management is key. Leading one of the world's largest firm with 85,000 employees is scary.
The pressure to achieve may ruin a day. Overworked employees are more likely to make mistakes or be angry with coworkers, according to the Family Work Institute. They can't handle daily problems, making the house more stressful than the office.
Walking your dog, having fun with friends, and having hobbies are as vital as your office.