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  • Madeline Topf

The BEST way to organize journal articles

When I was writing my thesis in college, I printed out every journal article I was reading. I highlighted and took notes on the page, scribbling into the margins diagonally. I kept every article in a big folder that I carried around everywhere and had to shuffle through to find something I needed. I have to say this is not the BEST way to organize journal articles....

Here are three ways I've tried and a new recommendation that takes minutes to set up. I use a Mac so maybe some of these are different with different operating systems.

1. Zotero

To be honest, I don't really get why anyone would use Zotero. It keeps the article title and pdf but the pdf opens in PREVIEW... and you can't really take notes on it. You can highlight on the preview, but then I have too many Preview tabs open and I can't ever tell if it's going to save ( I think it does).

You can add notes, but they have to be submitted as an attachment. I don't have a monitor, so I have to click around from my Preview page that is a pdf to the Zotero notetaker and it gets messy.

The look of Zotero is very clean, and the Google Chrome extension works really well to grab pdfs from your browser and organize them into folders. Folders are easy to make and organize and look very clean cut. I haven't used Zotero to manage citations/make a References section in Word.

Unfortunately my lab uses Zotero to keep and share citations.


2. Mendeley

I like Mendeley! It is basically Zotero but the pdf opens within the desktop application and you can easily highlight and take notes on the side that save. It's easy to make folders and organize everything.

The Chrome extension sort of works, it is very slow and sometimes can't find the pdf even if it's staring it in the face. The citation list in each folder looks less clean and simple and can feel very stressful and overwhelming if you don't take the time to sort them. But it is very nice to open multiple pdfs at once and read/take notes on them.

There is a Mendeley add-on to Word that works really well in formatting citations and adding the References in the correct style.


3. An Excel Database

My mental health may suffer by being on Academic Twitter but I have found some helpful tips on there. One of which is this so-chaotic-it's-good Excel Database created by Stephen McQuilliam.

Here is a youtube video showing how to make this thing. Essentially, you create categories and notes about all of your articles and input them into the database. Then, you are able to sort by these details to find specific articles you have.

I like this idea a lot because it will show papers I didn't remember I had read or that pertained to a specific method. For example, I can search for all the papers in my database that use Nanopore sequencing of gut bacteria. I might find a paper about Nanopore sequencing of environmental Staphylococcus that I had saved for a separate project in lab. It's still useful because it is related to a method I'm interested in, even if it is unrelated to the specific topic.

The downside, of course, is that you have to input all of the papers and all of the information about them manually. I set it up really easily but haven't touched it since. It would take a lot of dedicated effort to upkeep the database, but it may pay off hugely in the end.


I think my favorite so far is still Mendeley, at least until I become more proactive and diligent. All are better than shoving print-outs into your backpack.

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