How to create a workflow to support your research and knowledge creation efforts (Obsidian app)

Summary

In this insightful video, computer science researcher Bianca Pereira shares her academic workflow, designed to balance note-taking and knowledge creation. She discusses organizing sources with the concepts of 'library' and 'interlibrary,' using tools like Evernote and Pocket for initial capture and Obsidian for in-depth note-making. Bianca also highlights the importance of maintaining a knowledge graph, leveraging LaTeX for equations, and transitioning from notes to research papers using Overleaf. Her process emphasizes the power of plain text files in fostering a personal and empowering knowledge management system.

Takeaways

• 📚 Bianca Pereira, a computer science researcher, shares her academic workflow for managing research notes and knowledge creation.
• 🔍 She emphasizes the importance of organizing sources using the concepts of 'anti-library' (unread, but interesting materials) and 'library' (processed and noted materials).
• 🗂️ Bianca uses Evernote and Pocket for her inbox, where she collects potential sources of interest before organizing them into her 'interlibrary' and 'library'.
• 📱 She mentions using Obsidian for note-taking and knowledge management, with a backup system in place through Google Drive synchronization.
• 🖍️ Highlighting in PDFs is part of her extraction process, where she differentiates colors for various meanings to aid in note-making.
• 🔗 Bianca discusses the use of embedded queries in Obsidian to show backlinks and trace how different notes relate to a specific paper or concept.
• 📝 She stresses the significance of keeping a historical record of thoughts and data analysis, advocating for a method that preserves the evolution of ideas.
• 🧠 The development stage of her workflow includes writing LaTeX equations in Obsidian, facilitated by MathJax, for easier transition into LaTeX documents.
• 🔑 Bianca explains the process of creating a MOOC (Massive Open Online Course) with ideas per section of a paper, which she then transfers to Overleaf for final paper formatting.
• 📝 She prefers using LaTeX over Word for paper writing due to the ease of formatting and the ability to import markdown files directly.
• 🔄 Bianca acknowledges ongoing challenges, such as creating a mobile-friendly environment for note-taking and the need for further exploration in her workflow.

Q & A

What is the main challenge that Bianca faced during her research process?

Bianca faced the challenge of managing her research notes effectively, as she found it easy to create a mess of research notes during her PhD studies.

What is Bianca's academic workflow designed to facilitate?

Bianca's academic workflow is designed to facilitate the process of knowledge creation while maintaining a balance between note-taking and note-making.

What are the two concepts Bianca introduced for organizing her sources?

Bianca introduced the concepts of 'anti-library' for books she plans to read and 'library' for books she has processed and taken notes on.

What tools does Bianca use for her inbox to capture sources?

Bianca uses Evernote and Pocket to create her inbox for capturing sources that she finds interesting.

How does Bianca categorize her notes after processing the inbox?

After processing the inbox, Bianca categorizes her notes into the 'interlibrary' and then into her 'library' using Obsidian.

What is the significance of the 'embedded queries' feature in Bianca's workflow?

The 'embedded queries' feature in Obsidian allows Bianca to see all the notes that are linked to a specific paper, helping her to track the usage and connections of her sources.

Why does Bianca prefer using LaTeX over Word for writing papers?

Bianca prefers LaTeX over Word because formatting is easier in LaTeX, and it allows for a smoother transition from markdown files to the final paper format.

How does Bianca integrate her notes into her knowledge graph?

Bianca integrates her notes into her knowledge graph by creating a MOOC for each section of the paper she wants to write, and then transferring the notes into Overleaf for further development.

What is the importance of keeping the history of thoughts in Bianca's workflow?

Keeping the history of thoughts is important in Bianca's workflow as it helps in understanding how ideas were constructed and allows for better analysis and data clustering.

What is Bianca's stance on writing papers in Word?

Bianca is against writing papers in Word due to the difficulty in formatting and prefers using LaTeX for its ease of use and integration with markdown files.

What open questions does Bianca still have regarding her workflow?

Bianca still has open questions about creating a good mobile environment for her notes, as she doesn't want all her notes on her mobile but would like to have them directing Obsidian.

Outlines

00:00

📚 Academic Workflow and Knowledge Creation

Bianca Pereira, a computer science researcher, discusses her academic workflow designed to balance reading and writing. She emphasizes the importance of organizing sources and notes, introducing the concepts of 'anti-library' and 'library' to manage unread and read materials, respectively. Bianca uses tools like Evernote and Pocket for her inbox and Obsidian for processing and storing notes, ensuring a synchronized backup with Google Drive. She also highlights the process of extracting information from readings, creating summaries, and analyzing content, which is crucial for knowledge creation and output.

05:02

🔍 Note-Making and Knowledge Graph Development

In this section, Bianca explains her method of note-making and the development of her knowledge graph. She uses Obsidian to create notes with embedded PDFs and links to the original sources, allowing for a visual representation of backlinks to specific papers. Bianca also discusses the importance of keeping the history of thoughts and data analysis, advocating for a method that retains the evolution of ideas rather than just the final summary. She mentions the use of LaTeX in Obsidian for writing equations and the transition of notes into a research paper using Overleaf, emphasizing her preference for LaTeX over Word due to formatting ease.

10:02

📝 Research Paper Creation and Mobile Environment Setup

Bianca outlines her process for creating research papers, starting with the compilation of ideas per section in a MOOC and then transferring them into Overleaf for formatting and compilation. She also addresses the challenges of setting up a mobile environment for note-taking, expressing her desire for a directed approach in Obsidian on mobile devices. The summary concludes with Bianca's invitation for further discussion on her workflow and an open acknowledgment of the many questions and areas for improvement that remain in her process.

Keywords

💡academic workflow

An academic workflow is a structured process researchers follow to manage their research activities, from reading and note-taking to writing and publishing. In the video, Bianca Pereira discusses her personalized academic workflow to efficiently organize her research materials and maintain links between her notes and the academic literature.

💡note-taking

Note-taking refers to the process of recording information from various sources. In Bianca's workflow, note-taking involves capturing ideas and information from academic papers and organizing them in a system like Evernote and Pocket for initial processing.

💡note-making

Note-making is the process of synthesizing and creating new knowledge from the information gathered during note-taking. Bianca highlights how she transforms her notes into a coherent structure using tools like Obsidian, making them part of her 'library' after processing.

💡anti-library

An anti-library consists of books or resources that one has collected but not yet read. Bianca uses this concept to distinguish between materials she intends to study (anti-library) and those she has processed and taken notes on (library).

💡Obsidian

Obsidian is a note-taking and knowledge management tool that uses plain text markdown files. Bianca utilizes Obsidian to organize her processed notes and create a knowledge base, linking her research insights with the academic literature.

💡Evernote

Evernote is a note-taking app used for capturing and organizing information. In Bianca's workflow, she uses Evernote as an inbox for her initial notes and ideas, which she later processes and moves to Obsidian.

💡knowledge graph

A knowledge graph is a network of interconnected information that represents relationships between concepts. Bianca builds a knowledge graph in Obsidian to link her notes and ideas, facilitating better understanding and retrieval of information.

💡latex

LaTeX is a typesetting system commonly used for academic and scientific documents. Bianca prefers writing her papers in LaTeX using Overleaf, as it allows for better formatting and integration of equations and references compared to word processors.

💡Markdown

Markdown is a lightweight markup language used for formatting plain text. Bianca uses Markdown in Obsidian to create and organize her notes, which she can then easily transfer to LaTeX for academic writing.

💡Overleaf

Overleaf is an online LaTeX editor that facilitates collaborative writing and publishing of academic documents. Bianca uses Overleaf to compile her Markdown notes from Obsidian into well-formatted academic papers.

Highlights

Bianca Pereira's academic workflow is a capstone project that she is still building, aiming to facilitate her process of knowledge creation.

Bianca uses the concepts of 'library' and 'interlibrary' to organize her sources, distinguishing between unread and processed materials.

She utilizes Evernote and Pocket for her inbox, where she collects potential research materials before processing them.

Processed materials are moved into her 'interlibrary' and then into her 'library' using Obsidian, a note-taking and knowledge management tool.

Obsidian is used for creating detailed notes with bibliographic information, summaries, and analysis, linked to the original PDF sources.

Bianca emphasizes the importance of keeping a history of thoughts and data analysis within her notes for research integrity.

She discusses the use of embedded queries in Obsidian to show backlinks and context of linked notes.

Bianca integrates her notes into a 'knowledge graph,' a knowledge base where the same code may appear in different notes depending on the context.

Obsidian's MathJax integration allows for writing LaTeX equations, facilitating the transition to LaTeX for academic papers.

Bianca prefers using LaTeX over Word for writing papers due to the ease of formatting and the ability to import markdown files.

She mentions the use of Overleaf, an online LaTeX editor, for compiling papers in the required format for conferences.

Bianca's workflow includes creating a MOOC (Massive Open Online Course) with ideas per section of the paper she intends to write.

She discusses the challenges of creating a good mobile environment for note-taking, as she prefers not to have all notes on her mobile device.

Bianca is currently working on publishing her workflow and aims to create an example for others to see how she organizes her research.

The transcript showcases the powerful use of plain text files at the core of research and knowledge creation.

Bianca's process demonstrates a healthy balance between note-taking and note-making for researchers.

The video aims to inspire viewers on how empowering and personal the process of thinking and managing knowledge can be.

Transcripts

are you an academic or researcher

struggling to balance what you read

versus what you write how do you strike

the right balance between note taking

and note making in the following

showcase bianca pereira shows away

bianca is a researcher in computer

science with an interest in knowledge

graphs data semantics and engaged

research during her phd studies she

discovered how easy it was to quickly

create a mess of research notes so in

this video bianca will show how she

created a complete academic workflow to

facilitate her process of knowledge

creation while also showing the links

between her work and the academic

literature from anti-library to notes to

knowledge creation and to output let's

view bianca's process now the workflow

itself the academic workflow is my

capstone project so i'm still slowly

building that so i'll try to do an

overview and then maybe after we can

have more conversations because our time

is very short today so

based on that uh the step by step that

nick has showed before like capture

extracting development creation

i try to kind of like map what are the

things that i have been currently doing

and i still have many questions many

open questions so the first thing

that was interesting for me especially

from the

conversations in this course is like how

can we capture our sources because when

you're doing research or academic work

our sources are very important and we

want to keep a link of them and organize

them and everything

before i have a mess in evernote like as

we all have

now i'm trying to divide these things

i have two concepts that are called the

library and the interlibrary so for

example if you see those books that i

have here they are mostly my auntie

library which means like things that i

have created and i say i really have

interest in reading them they are good

quality

but i haven't read them yet so they are

on the things that i will study

where the things that i have processed

that i have had thoughts about them i

took notes they become my library so i

have this concept when i work with

research and it's important to have an

inbox where it's just where you just

throw stuff that you saw like ah this

paper may be interesting you put a small

note

and so then i'm trying to this is to

unorganize it in my case so i use

evernote and pocket

to to do the inbox and after processing

the inbox something is going to the

interlibrary

and when i decide okay i read this paper

now then i move that into my library

using obsidian so i have here

one uh folder

which is for files and i put all the

files in there

so i have like people

i have invoices that have papers here

so

after having

those things in obsidian i do a backup

always with everything is synchronized

with my google drive so i always have

this

on my phone or other computer

and

then comes the process okay now that i'm

i'm reading that whatever do i get the

pdf which i can read on my phone

i don't know how to pronounce shadow or

preview on mac and i have different

colors of highlighting meaning different

things

and then from that comes the first part

of extraction which i do in obsidian

so one example

of is this note for example

so i have some bibliographic information

rather than having text i have a big

text

then i put what is the pdf document so

you are able to see the pdf here

and then the original source

my summary

some analysis something that i was

trying to do today actually

i don't know it's true enough you know

what is the idea of embedded queries

okay

i don't know why it's not working now it

was working

two hours ago

maybe my query now is just

i just look like this

so basically what it does just showing

the back link so you can see all the

notes that have linked to this specific

uh

paper

so i would like to have the extracting

the piece here

but so far is just like the

words that appear in the context of the

link but i can still pass the the mouse

on that basically the same thing that

they have in the backlinks but i think

it's good at some point they say okay

this source where where

where it has been and what is it so

basically you just put as you are you

are putting common block or like code

block

and you just write query and then you

write query as you would write

in this

so you can write

you can use path file tags lines you can

remove things i was trying for example i

don't want to have my

my daily journals for example so i just

say i don't want anything with the tag

journal

so my daily journals don't appear

anymore

so

maybe i don't want my sources as well so

i can just that's what i was trying but

it didn't work i don't know

i don't want my source

now it's working so it do not appear

other papers because i all i tag them

always source or you can say everything

that is in i just want things that are

in this there are in this folder so

there are multiple ways to to do that

i think and here i just put the pdf so

that's one of the things and what i do

the same thing here i put as an elias

and i'll show later when i talk about

latex and publication why i try to do

that

so

as i read and i was creating my notes i

i have always the notes in

my thoughts in the note itself of the

paper and

i already move into my what i call my

knowledge graph which is the knowledge

base itself where the same code may

appear in different notes depend on the

context and with some comments about

that but they always appear in the

original one as well

then

uh

in the development stage

something for people especially who

write the questions we can write latex

equations in obsidian okay because it

has method mathjax

which is a javascript

library that parse

equations so you can have those things

in obsidian

and then after if you want to write in

latex it's much easier because already

in latex

um

and then some of the things that i found

i find important when working on my

knowledge base in obsidian

is the idea of keeping history because

when you are talking about moocs we say

we collide the the thoughts we just

break notes into delete notes and

the deleting part was really hard for me

because you want to keep the history of

things and that's where i was finding

the the comment from the disco in the

discourse uh from ujj and she was like

but i say things just in case but our

just in case is really because

we care about the history how how was

this thought constructed

so for example especially when you're

doing data analysis from the from

inductive perspective so it's like more

bottom up

so

rather

let's stay with the final version and

throw everything away i will have just

one note

which is not even none of those which is

just the summary of my results

but for research you want to say okay in

the first stage my raw data in the

circle stage how did i analyze what are

the results and the link with the

original raw data

and then stage two how the did i cluster

those things how they relate to the

original so all those things have links

unfortunately i cannot show them at the

moment because it's still not published

i would like to

but for the capstone i'll create at

least an example so you so you'll be

able to see how i do that

um

so yeah then i think that the idea of

moocs or the emergence is like if you

are doing deductive research

it's good to start from moocs or

something more high level then you go

breaking down

on what you're trying to do and the

inductive is always good also good but

keeping these links all the way up

and then after having written everything

marked down in obsidian

then the last step so i say like i

create a mooc

with all the ideas per section of the

paper that i want to write let's say

introduction

those are the ideas which was something

i was talking yesterday

and then after i can even write each

section of the paper itself as different

notes in obsidian

and then i can transfer them into

overleaf because

overleaf

uh for for those who use latex i don't

use words i never write papers in words

i'm against writing papers and words

because formatting is really hard in

word

so in latex you just have you just

change the template which they usually

come given by the conference and you can

actually just import your markdown files

so basically having markdown files you

use package hybrid markdown

and then you just import them and then

you just say mark the input and it says

the name of the file

and then when you recompile to generate

the pdf so i have this note here

it's just narrow mark down i just took

from obsidian

and and uploaded so the introduction and

then what happens here

my

introduction

is there on the format

of the conference

the

subtitle important point the same thing

and then

i need to check through the equations

okay i put like a episode equation here

and as it was already in latex it

already appears here so there are still

a few things like you cannot use the

media wiki type of links

you need to use the normal markdown

links otherwise it doesn't work there is

a trick also to put the images here you

just need to have one piece of uh

in the original latex and then to show

the image in the two columns one

but i can share those things with you in

this course later like how to write them

and there are still many open questions

like how to create a good environment

for the

for the mobile because we don't have

obsidian i don't want to have all my

notes in the mobile but i would like to

to have the nose directing obsidian

and

yeah i still have many things to talk

about

well i suppose

my time ago

seeing bianca's whole workflow shows

what's possible for researchers using

obsidian why is that so important

because she shows how you can powerfully

use plain text files at the core to

research and create knowledge that you

can grow into a research paper a

master's thesis or even a phd

dissertation bianca shows how the

researcher can cultivate a healthy

balance between note taking and note

making as always there are so many more

fascinating people i hope to showcase

with you because they show how

empowering and personal the process of

thinking and managing knowledge should

be what did you like most about bianca

showcase let me know in the comments

below and until next time stay connected