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Identifying Research Gaps and Questions with ChatGPT and Draw.IO

Every academic is looking for research gaps and open questions in their field. What if we could automate this in part by leveraging ChatGPT? This workflow will transform 20 loose pages of notes into an AI-generated mind-map. Research questions and gaps start to emerge automatically as we work with the visual diagram. Save yourself some anxiety and embarrassment as you say goodbye to disconnected Post-Its, Zotero annotations, and loose Microsoft docs.

Spot Research Gaps with AI Mindmaps

We will use a diagramming Draw.IO to organise and compile all your scattered notes and literature readings into one visual chart. You can easily identify research gaps and questions in five steps:

  1. Gather notes to create a research summary using ChatGPT
  2. Create a mind map using ChatGPT and Draw.IO
  3. Prompt ChatGPT to identify research questions from your summary and add it to the diagram
  4. Prompt ChatGPT to identify research gaps from your summary and add it to the diagram
  5. Design and re-arrange the final mind map

Before we get started, I invite you to subscribe to the Effortless Newsletter.

Step 1: Let’s create a research summary to feed into ChatGPT

You’ve done weeks of reading, and note-taking, and you feel lost in the weeds. You need to see the big picture once again. Let’s create a research summary from your accumulated and loose collection of notes. ChatGPT can summarise an overview and a status update of the long pieces of text (including draft manuscripts and scientific journal articles) that you have been writing down for weeks or months.

This is an example of what my notes look like from my Obsidian vault. It is okay if your notes are a combination of a numbered format, phrases, keywords, or acronyms.

Cut and paste your notes into a word processor to determine the word count

Use software that gives you a word count. Keep your notes under 3,000 words for the free version of ChatGPT 3.5. You can have as much as 25,000 words for ChatGPT 4.

Make sure you can track where you left off and where you want to continue again.

For example, Microsoft Word has a word count below the document screen.

You can find the word count of Microsoft Word at the bottom of the screen

If you highlight a block of text, Microsoft will count the words in the highlight and still show the total word count.

Paste your text into the ChatGPT window to generate your research summary

Once you select your text, paste it to the ChatGPT window. Ask ChatGPT for a summary. Use the simple prompt, “summarise.” You can see in my video that the text I inputted is very long. If you pause in the last second of the video, you can see how concise and short the ChatGPT summary is. Now you have an updated research summary.

Creating a research summary with ChatGPT using your notes.

However, this is not very useful yet if we want to identify missing connections and gaps. Our thinking processes rely on relationships and connections between ideas and concepts. This is the basis of the Effortless Note Taking system where connected reading and thinking form the bedrock of note-taking.

Step 2: Create a mind map from your text summary using ChatGPT

Once you obtain ChatGPT’s summary, paste it into your own note-taking system. Since this is based on YOUR content, you can have a higher degree of trust with the results. Use this to clean and review the status of your own research. Additionally linking connected concepts in your vault helps “anchor” this summary in the context of your research.

Summaries of your own work that you touch up manually or create from scratch are a great way or refreshing your memory and quite often creates new ideas – especially as the number of your notes starts to grow.

An example of an AI generated note and then stored in Obsidian so you could link key concepts into your notes

Feed ChatGPT with this prompt to produce a diagram syntax code

Once you have reviewed your text, let’s convert your research summary text into a visual chart. ChatGPT is great at generating a text-based diagram format called a mermaid diagram. We will take this code and translate it into a visual diagram next.

Here is a prompt to create the diagram:

Create a mermaid diagram out of the core concepts in this context and annotate the connections. Make sure that all relevant concepts are mentioned in the diagram. Make sure that the mermaid diagram: 1. Uses quotation marks around the connections 2. The node descriptions do not contain any parenthesis or special characters 3. That each line ends in a semicolon

Copy ChatGPT’s visual summary syntax code

Once you hit enter, ChatGPT will give you this code as a result. Copy the code with the button at the top right. We will use this to paste into a free diagramming tool called Draw.IO.

An example of how ChatGPT generates syntax code for a mermaid diagram ready to be placed in any software

Paste mermaid code into Draw.IO to display the initial mind map

Draw.IO is a free tool that you can use to create very elaborate diagrams and is indispensable to make sense of a big body of knowledge. If you link your account, you can save your drawings instantly in your preferred cloud drive. Or download the tool to your hard drive to work offline.

A really cool feature is that you can save your diagrams as editable SVG images. Those SVG images can be embedded into obsidian just like any other image. So you end up with an image directly in your notes, that you can keep editing with drawio at any point – perfect for what we are trying to do here.

To paste ChatGPT’s code results, use the toolbar on the top then click “Arrange” > “Insert” > “Advanced” > “Mermaid”. Here is a video of this hidden gem of a feature:

Once you see the pop-up box, paste the ChatGPT code into it and hit OK. The result is a little bit messy, but it can be easily styled later. You may play around with your diagram and use it as part of your initial review.

💡 Troubleshooting:

If you receive an error message like this, don’t panic!

What do I do if I receive a syntax error on Draw.IO?

Copy and paste this error message into ChatGPT asking it to fix it. Usually it will correct the syntax error and produce a corrected version. Repeat the previous step.

If the problem persists, ChatGPT will give you multiple syntax versions to try again. Some versions are readable and useful to create manual charts with, like this:

ChatGPT can correct its syntax errors and produce simple mermaid diagram for Draw.IO

The best way to store your diagram is as an SVG file. This format will generally result in the smallest filesize and is editable by Drawio. Other options like JPG,PNG etc are available.

Step 3: Ask ChatGPT to generate research questions using your own notes

You can formulate your own questions as specialist and expert in an area. However, if you work in interdisciplinary domains, you may not be cognizant of your own knowledge gaps. And your colleagues may feel the same way. Some questions may be obvious, some may not.

Enter ChatCGPT which can pull out the questions hidden in your notes that you are not aware of.

Using the previous mermaid diagram syntax, copy this prompt to the next message box. ChatGPT will deliver a new set of diagram syntax that you can then paste again to Draw.IO.

ChatGPT prompt to generate research questions from your own notes. The syntax code will be used to paste in Draw.IO

ChatGPT added a few more lines to the diagram, which will correspond to new nodes. The capital letters will help you distinguish them from the general notes.

Step 4: Asking ChatGPT to generate research gaps using your own notes

Using the same diagram syntax, I am going to set more tasks for ChatGPT. This time I want it to examine connections from my notes that I may not have noticed. Follow the prompt below:

Use ChatGPT to generate research gaps from your notes. The syntax code can be used to paste to Draw.IO and create a mermaid diagram

ChatGPT gave me another four nodes indicating knowledge gaps in my notes. It connected them to other separate categories. To not confuse me, I prompted ChatGPT to “make the four nodes representing gaps in my knowledge all CAPS.” I simply re-used the words of ChatGPT to prompt it.

We now have our final diagram, it is time to just touch up on int aesthetically.

Step 5: Design your Mindmap for clarity and visibility

Let’s fix the diagram to make it clear for you and your intended audience.

How to colour-code your research questions and research gaps in Draw.IO

Select the QUESTION boxes and use the style panel on the top right of Draw.IO to colour them green. Select the GAPS boxes and colour them red. DrawIO has some predefined styles at the top right. Here is how the result might look:

Color code your research questions and gaps in the mermaid diagram

How to straighten your connecting lines and add text boxes on Draw.IO

Find your stylistic preference. But I find straight connecting lines make it less distracting for viewers especially if you are adding more text boxes.

Click on a line or connector. The pop-up box “Line” will appear to your right. Select the straight feature.

You can select all lines at once by clicking “Edit > Select Edges” in the main menu of DrawIO. So you don’t have to repeat this step for all connections manually.

How to fix your connector lines to become straight at Draw.IO

There are many tutorials on using out there, while it takes some time to get used to, it becomes a very handy ad useful tool over time.

Re-arrange your research gaps and questions on the outer borders of your mind map

After colour-coding, you need to judiciously arrange your diagram boxes to avoid confusion for yourself and your audience. I usually place my research questions (in green) on top while the research gaps (in red) are at the bottom. At a glance, I can quickly guide my eye and help me when I am presenting, discussing, and sharing my initial findings with myself and my audience.

Final AI generated research gaps and questions from your own notes and rendered in a mermaid diagram


In this workflow we used ChatGPT to summarize a set of loose notes into a shorter text. Then we extracted core concepts out of it and automatically arranged them in a diagram format called mermaid. These diagrams can be readily pasted into free diagraming tools like and if you want to even Obsidian itself.

ChatGPT can help identify research gaps and questions and add them to our diagram.

Needless to say that you should never rely on ChatGPT to make an entirely meaningful discovery or be exhaustive in its gap analysis. In the near future however tools like ChatGPT might get powerful enough to make significant contributions. Until then, use the workflow to save some time and see your research “through a fresh pair of eyes”.

Your results however will be only as good as your notes. Streamline your reading and writing workflow using the Effortless AI Literature Review and Effortless Academic Manual programs to make your notes work three times as hard for you.