Sharing best practices on academic writing research papers (qualitative)

Hello fellow Obsidianers,

I struggle to write a research paper (qualitative case study, to be more precise) in Obsidian, always switching to MS Word simultaneously. The reason is that when I have a research paper idea/article, I create a new note with an article in the name of the note and the title of the article. Afterwards, as you all know, there are sections and subsections that include an introduction, theoretical lens, etc. Then I start writing each section inside that one note; however, when I write something, I want to keep it and remember it, and sometimes I make it a backlink (with []). As time passes, I have a lot of ideas, and then I find it a mess, where sometimes I backlink something, sometimes the title of the note is too general, and I cannot find it easily when I need it. The reason behind this is that the title of the note is too big, doesn’t always represent what is inside the note, and contains many paragraphs that I cannot use afterwards. Or if I write an introduction, I have some annotated research papers that I cannot find, or I don’t remember what was in it.
This is my experience, so I was wondering how you write your research papers. Do you make minor notes or the whole paper (just like in MS Word) inside one note?
I am very interested in reading how you do it and exchanging best practices.


It sounds like you’re grappling with organization and structure in your research paper writing process. Here’s my suggestion that might help streamline your workflow and maintain clarity:

  • Break Down Your Notes: Instead of writing entire sections of your paper within a single note, break them down into smaller, more focused notes. For example, have separate notes for your introduction, theoretical framework, methodology, findings, etc. This way, each note will contain specific and manageable chunks of information.
  • Clear and Specific Note Titles: When creating a new note, ensure that the title is clear and specific to the content it will contain. Avoid overly general titles that might become confusing later on. If necessary, you can always add more specific tags or metadata to help with organization and retrieval.
  • Utilize Backlinks: Continue using backlinks to connect related ideas and notes. However, instead of embedding them directly within your text, consider using them sparingly or creating a separate section at the end of each note for related backlinks. This can help keep your main text focused and reduce clutter.
  • Annotate Research Papers Effectively: When annotating research papers, make sure to include clear and concise summaries of the key points or findings. Consider using a consistent format or template for your annotations to make them easier to review later on. You can also include tags or links to relevant notes within your annotations for easy reference.
  • Regular Review and Cleanup: Set aside time regularly to review and organize your notes. This could involve renaming or reorganizing notes as needed, adding additional tags or metadata for better categorization, and consolidating related notes. By maintaining your Obsidian vault regularly, you can prevent it from becoming cluttered and make it easier to find the information you need.

Satisfied with my answer? Or do you have any further questions?


Thank you Edmund for your suggestions!

Indeed, I struggle with organisation and structure in my paper.

I have to mention that the last point on Regular Review and Cleanup is the most important point. Primarily because I have many concepts, annotated notes, that I rarely go back and check them.
So I guess I have to go and clean up my vault significantly.

Another point, is the clear and specific note titles. Could you please elaborate more on that? What for you would be a clear and elaborate note if you write an introduction section for your paper, or even theoretical framework?

At the end, how do you follow up on the arguments positioned in introduction to the discussion section in another note? Do you backlink (![] ) or you do something else?

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Certainly! Clear and specific note titles are essential. Here’s how you may create note titles for different sections of your paper:

Introduction Section: A clear and specific note title for the introduction section could include the following elements:

  • Topic or main focus of the introduction
  • Purpose or objective of the introduction
  • Any key concepts or theories introduced in the section For example: “Introduction - Overview of Research Topic and Objectives”

Theoretical Framework: For the theoretical framework section, consider including:

  • The name of the theory or theories being discussed
  • Key concepts or components of the theoretical framework
  • Any specific frameworks or models referenced For example: “Theoretical Framework - Application of Social Cognitive Theory in Understanding Behavior”

When transitioning from one section to another, such as from the introduction to the discussion section, you can maintain coherence by using Backlinks or Cross-Referencing:

  • Backlinks: You can use backlinks to connect related sections or arguments across different notes. For example, in the discussion section note, you can include backlinks to relevant points or arguments introduced in the introduction. This allows you to easily navigate between different sections and ensures continuity in your arguments.
  • Cross-Referencing: In addition to backlinks, you can also explicitly refer to specific points or arguments from one section to another within your text. This can help reinforce connections between different parts of your paper and provide a clear pathway for readers to follow your reasoning.

The key is to find a system that works best for you and supports your writing process effectively. So it is useful to experiment with different techniques until you find a workflow that helps you stay organized and focused throughout your writing process.