How to create a workflow to support your research and knowledge creation efforts (Obsidian app)
Summary
TLDRIn 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
📚 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.
🔍 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.
📝 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.
Mindmap
Keywords
💡academic workflow
💡note-taking
💡note-making
💡anti-library
💡Obsidian
💡Evernote
💡knowledge graph
💡latex
💡Markdown
💡Overleaf
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
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