Doing a literature review using digital tools (with Notion template)

I’ve recently revamped my literature review workflow since discovering Notion. Notion is an organization application that allows you to make various pages and databases. It’s kind of like your own personal wiki- you can link your pages and embed databases into another page, adding filters and sorting them using user-set properties. The databases are what I use the most. I’ve essentially transferred all of my excel sheets into Notion databases and find it much easier to filter and sort things now. In this post, I’ll go through how I do my literature review and share a Notion template that you can use.

I like to organize my literature review using various literature review tools along with two relational Notion databases: a ‘literature tracker’ and a ‘literature notes’ matrix. You can see a flow chart of my literature review process below (it’s inspired by this post by Jenn’s Studious Life and the three pass method for reading papers which I wrote about last week in this post):

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As you can see, this process involves a couple of decision points which helps me focus on the most important papers. This is an iterative process that keeps me up to date on relevant research in my field as I am getting new paper alerts in my inbox most days. I used this method quite successfully to write the literature review for my confirmation report and regularly add to it for the expanded version that will become part of my PhD thesis. In this post, I’ll break down how this works for me and how I implement my Notion databases to synthesise the literature I read into a coherent argument.

You can click on the links below to navigate to a particular section of this article:

The literature search

The literature tracker

The literature synthesis matrix

Writing your literature review

Iterating your literature review

My literature review Notion template

Some useful resources

The literature search

This is always the first step in building your literature review. There are plenty of resources online all about how to start with your search- I find a mixture of database search tools works for me.

The first thing to do when starting your literature review is to identify some keywords to use in your initial searches. It might be worth chatting to your supervisor to make a list of these and then add or remove terms to it as you go down different research routes. You can use keyword searches relevant to your research questions as well tools that find ‘similar’ papers and look at citation links. I also find that just looking through the bibliographies of literature in your field and seeing which papers are regularly cited gives you a good idea of the core papers in your area (you’ll start recognising the key ones after a while). Another method for finding literature is the snowballing method which is particularly useful for conducting a systematic review.

Here are some digital tools I use to help me find literature relevant to my research questions:

Library building and suggestions

Mendeley was my research management tool of choice prior to when I started using Notion to organize all of my literature and create my synthesis matrix. I still use Mendeley as a library just in case anything happens to my Notion. It’s easy to add new papers to your library using the browser extension with just one click. I like that Mendeley allows you to share your folders with colleagues and that I can export bib.tex files straight from my library into overleaf documents where I’m writing up papers and my thesis. You do need to make sure that all of the details are correct before you export the bib.tex files though as this is taken straight from the information plane. I also like to use the tag function in Mendeley to add more specific identifiers than my folders.

Mendeley is also useful for finding literature related to those in your library- I’ve found quite a few interesting papers through the email updates they send out each week with ‘suggested papers’. You can also browse these suggestions from within Mendeley and use its interface to do initial keyword searches. The key is to just scan the titles and then decide whether it’s worth your time reading the abstract and then the rest of it. It’s easy to get overwhelmed by the sheer amount of papers being published every day so being picky in what you read is important (and something I need to work on more!).

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Some similar tools that allow you to build a library and get literature recommendations include Zotero, Researcher, Academia, and ResearchGate. It’s up to you which one you use for your own purposes. One big factor for me when choosing Mendeley was that my supervisor and colleagues use it so it makes it much easier to share libraries with them, so maybe ask your colleagues what they use before settling on one.

Literature databases and keyword alerts

There are a variety of databases out there for finding literature. My go-to is Web of Science as it shows you citation data and has a nice interface. I used this to begin my initial literature search using my keywords.

The other thing you can do with these kinds of tools is set up email alerts to get a list of recent work that has just been published with any keywords you set. These alerts are usually where I find papers to read during journal club with my supervisor. You can customize these emails to what suits you- mine are set to the top 10 most relevant new papers for each keyword weekly and I track around 5 words/phrases. This allows me to stay on top of the most recent literature in my field- I have alerts set up on a variety of services to ensure that I don’t miss anything crucial (and alerts from the ArXiv mean I see preprints too). Again, you need to be picky about what you read from these to ensure that they are very relevant to your research. At this stage, it’s important to spend as little time as possible scanning titles as this can easily become a time suck.

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Some of the other tools I have keyword (and author) email alerts set up on are: Scopus, Google Scholar, Dimensions, and ArXiv alerts. I set 10 minutes maximum aside per day to scan through any new email alerts and save anything relevant to me into my literature tracker (which I’ll come to more later).

Literature mapping tools

There are loads of these kinds of tools out there. Literature mapping can be helpful for finding what the seminal papers are in your field and seeing how literature connects. It’s like a huge web and I find these visual interfaces make it much easier to get my head around the relationships between papers. I use two of these tools during the literature search phase of the flowchart: Citation Gecko and Connected Papers.

Citation Gecko builds you a citation tree using ‘seed papers’. You can import these from various reference management software (like Mendeley), bib.tex files or manually search for papers. This is particularly useful if your supervisor has provided you with some core papers to start off with, or you can use the key papers you identified through scanning the bibliographies of literature you read. My project is split into fairly clear ‘subprojects’ so these tools help me see connections between the various things I’m working on (or a lack of them which is good in some ways as it shows I’ve found a clear research gap!).

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You can switch between different views and add connecting papers as new seed papers to expand your network. I use this tool from time to time with various different papers associated with my subprojects. It’s helped me make sure I haven’t missed any key papers when doing my literature review and I’ve found it to be fairly accurate, although sometimes more recent papers don’t have any citation data on it so that’s something to bear in mind.

Connected Papers uses a ‘similarity’ algorithm to show paper relationships. This isn’t a citation tree like Citation Gecko but it does also give you prior and derivative works if you want to look at them. All you do is put one of your key papers into the search box and ‘build a graph’. It will then show you related papers, including those which don’t have direct citation links to the key paper. I think this is great for ensuring that you’re not staying inside an insular bubble of the people who all cite each other. It also allows me to see some of the research which is perhaps a bit more tangential to my project and get an overview of where my work sits within the field more broadly.

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I like Connected Paper’s key for the generated tree and that it shows where related papers connect between themselves. Again, it’s helpful for ensuring that you haven’t missed a really important work when compiling your literature review and doesn’t just rely on citation links between papers.

The literature tracker

This is where I record the details of any paper I come across that I think might be relevant to my PhD. In some ways, it’s very similar to Mendeley but it’s a version that sits within Notion so I have some more customised filtering categories set up, like my ‘status’ field where I track which pass I am on.

Here’s what my literature tracker looks like:

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The beauty of Notion is that you can decide which properties you want to record in your database and customize it to your needs. You can sort and filter using these properties including making nested filters and using multiple filters at once. This makes it really easy to find what you’re looking for. For example, say I’m doing my literature review for my ‘FIB etching’ subproject and want to see all of the papers that I marked as relevant to my PhD but haven’t started reading yet. All I need to do is add a couple of filters:

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And it filters everything so that I’m just looking at the papers I want to check out. It’s this flexibility that I think really gives Notion the edge when it comes to my literature review process.

The other thing I really like about using Notion rather than excel is that I can add different database views. I especially like using the kanban board view to see where I’m at with my reading workflow:

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When I add something to the literature tracker database, I scan the abstract for keywords to add and categorize it in terms of relevant topics. It’s essentially the first pass of the paper, so that involves reading the title, abstract, introduction, section headings, conclusions, and checking the references for anything you recognise. After this is done, I decide whether it’s relevant enough to my PhD to proceed to do a second pass of the paper, at which point I will progress to populating my literature notes database.

The literature synthesis matrix

Once I’ve decided that I want to do a second pass on a paper, I then add it to the ‘literature notes’ database. This is part of the beauty of Notion: relational databases. I have ‘rollup’ properties set in the literature notes database which shows all of the things I added during my first pass and allows me to filter the matrix using them. You can watch the video below to see exactly how to add a new paper to the ‘notes’ database from the ‘tracker’ database:

During the second pass, I populate the new fields in the ‘notes’ database. These are:

Summary | Objective of study | Key Results | Theory | Materials | Methods | Conclusions | Future work suggested | Critiques | Key connected papers.

I also have various themes/questions/ideas as properties which I add a few notes on for each relevant paper. I then complete my ‘questions for critical engagement’ which are on the entry’s ‘Notes’ page and are stored in the ‘Article Template’. If you want to read more about this process, check out my ‘how to read a scientific paper’ post.

By, doing this I create a synthesis matrix where I can see a breakdown of the key aspects of each paper and can scan down a column to get an overview of all of the papers I have read. For example, if I wanted to see all of the papers about Quantum Point Contacts to get an idea of what previous work has been done so that I can identify my research gap, I can filter using the tag property and can then see the notes I wrote for each entry, broken down by section. I also have tags for my research questions or themes, materials used, experimental techniques, fabrication techniques, and anything else that comes to mind really! The more tags I have for a paper, the easier it is to filter when I want to find a specific thing.

The other property I have included in the literature notes database is ‘Key connected papers’. This is a relation but is within the database itself. So it means that I can link to the page of other papers in the literature matrix. I’ve found this to be useful for connecting to what I call ‘core’ papers. I can also filter using this property, allowing me to see my notes on all of the papers I’ve read that are related to a certain ‘core’ paper. This helps with synthesising all of the information and forming my argument.

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For those papers most relevant to my research (the ‘core’ papers) I’ll also do a third pass which involves reimplementing the paper in my own words. This is quite a time-consuming task so not many papers reach this stage, but those which I have done a third pass on are the ones I know really well. My hope is that this will stand me in good stead for my viva. This process also helps me refine my research questions further as I gain a deeper understanding of the field.

Writing your literature review

I find that writing up a review is extremely intimidating, but having the literature matrix makes this process that bit easier. I won’t go into too many details as there are already loads of resources out there going into the details of writing up a review, but here’s a brief overview of my own process:

Identify your research themes

Using your literature matrix, review each research theme or question and decide which ones you are going to focus on. These will form the different sections of your literature review and help you write your thesis statement(s). You can also think about how your questions link to ensure that you’re telling a coherent story with your review.

Choose and summarize literature related to each theme

For each section, gather up the most important related literature and summarize the key points of each source. A good literature review doesn’t need to cover all the literature out there, just the most significant sources. I try to stick to around 10 or fewer key sources per section.

Critical evaluation of sources

This is where you utilize the ‘questions for critical engagement’. Make sure you evaluate the strengths and weaknesses of the studies you’re writing about. By doing this, you can establish where our knowledge is lacking which will come in helpful later when establishing a research gap.

Analyse each source in relation to other literature

Try to make sure that you are telling a coherent story by linking between your sources. You can go back to the literature matrix here and use it to group similar studies to compare and contrast them. You should also discuss the relevance of the source’s findings in relation to the broader field and core papers.

Situate your research in a research gap

This is where you justify your own research. Using what you have laid out in the rest of the review, show that there is a research gap that you plan to fill and explain how you are going to do that. This should mean that your thesis flows nicely into the next section where you’ll cover the materials and methods you used in your research project.

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Iterating your literature review

In some ways, a literature review never really ends. As you can see in the flowchart at the beginning of this post, I regularly update and revise my literature review as well as refining my research questions. At this point in my PhD, I think that most of my research questions are quite well defined, so I’m mostly just adding any newly published work into my review. I don’t spend much time reading literature at the moment but I’m sure I’ll return to it more regularly when I’m in the write-up phase of my PhD. There is a balance to be had between reading and writing for your literature review and actually getting on with your own research!

My literature review Notion template

Here’s the link to my Notion Literature Review Template. You can duplicate it and adapt it however you want, but this should save you some time setting up the initial databases if you’d like to use my method for organizing your own literature review.

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Some useful resources

Here are some resources on how to do a literature review that I’ve found useful during my PhD:

• The Literature Review: Step-by-Step Guide for Students
• 3 Steps to Save You From Drowning in Your Literature Review
• How to write a literature review
• How to become a literature searching ninja
• Mind the gap
• 7 Secrets to Write a PhD Literature Review The Right Way

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