|𝔻⟩irac's Student: Parsing research articles with a Zotero workflow

I started thinking about needing to document my reference and journal reading process since I may want to overhaul it later on based on the rapidly evolving tools that are coming out such as elicit.org or scispace.com. So here is how I do things for the most part.

My go-to reference manager: Zotero

If you are anyone who is conducting research in an academic, government, or even industrial lab setting you most likely are familiar with a reference manager. The list is exhaustive nowadays, but for me, there is only one that I've consistently kept going back to and that is Zotero. The thing I like about Zotero is that it's multiplatform, open-source, no-cost, easy to use, and has a good amount of features integrated. The biggest issue is the cloud storage cost. This is really only a problem if you want to have all your attached pdfs stored on the cloud service so that you can access them using the browser interface.

To get around this limitation you can use the ZotFile extension which allows you to change how Zotero stores and renames files. If your using Google Drive or DropBox, this means you can create a folder on your cloud storage and then use ZotFile to store all linked PDFs there. If you have multiple devices with the same OS and file structure, then opening the attached files on any of your devices with Zotero desktop will work. If this is not possible with your working environment, for example, you have Windows and Linux machines. Then you will just want to make sure you create links to your local cloud storage path for the Zotero entry. You could also open the folder on your cloud storage such that anyone with the links can access the files and then add these as links in the Zotero entry. That way your file is always accessible no matter where you try to grab it from.

There is one other Zotero add-on I like to use since I do a lot of my technical writing in LaTeX. The Better Bibtex extension makes generating .bib files extremely easy and . Furthermore, it makes using your preferred bib entry naming schema consistent across all references straightforward. You also don't have to worry about keeping a .bib file updated.

Grabbing Literature

There are several ways to get journal articles so I'm not going to list all of them. For me, the easiest and most natural is to just use google scholar. I like google scholar mainly because it grabs any PDFs that have been posted on the internet and ties them to the reference.

Parsing Literature

Once I've added an entry to my Zotero library, which includes adding relevant PDFs, GitHub repo links, and tagging, making sure you tag and grab relevant links will make it easier latter on. I then go about creating a note item for each entry. The nice thing with recent versions of Zotero notes is that they are markdown+rich text meaning you can be pretty detailed. So how do I initial parse without having to read all the papers I've added? I add three sections in the note. The first is a summary section. For this, I either use ChatGPT, SciSpace, or paper digest to do this for me. Then I look through the paper/document and screengrab any figures that stand out to me for whatever reason. Finally, I mark the priority level. Do I think this is a high-priority paper to read or not? The reason to do that in the note and not the tag is because the priority for reading is a transient state of an entry; it will change over time and eventually have a null status once it's read.

Once I'm done creating the notes, what I can do for a specific folder that may represent a topic or a specific project is generate a Zotero report that provides all the metadata text for the entries. I can then go through it again to see what stands out to me. This in my opinion is a really nice feature, because it lets me visually go through the titles and my notes and see what I want to focus on first. There are some fancy tools out there that can create graphs of connectivity and other relationships between papers which would probably also be very useful if your trying to narrow down papers to read.

Reading Literature

Once I'm done selecting which papers I want to read from the Zotero report I generated, I will then print out the papers. Yes, I know printing doesn't make much sense in our multi-monitor research setups, but for me, I can't seem to shake the desire to want to read a paper in physical form. There is something about being able to flip back and forth between different sections and how I represent concepts and results in my mind's eye. I believe there is some strong evidence for better information recall when reading books in physical form.

For reading the papers, there is no real best approach in my opinion, you just have to sit down and read in the best way that works for you. I personally try not to spend too much time marking up the document. I will typically just add some kind of marking to indicate to myself some passage or content I find interesting or important. Once I'm done reading I then go to the digital PDF of the paper in Zotero and make annotations and highlights of the parts I've indicated on the physical form. This is important because when I'm writing and want to reference the document, I use these annotations and highlights as a guide for why I wanted to reference the paper in the first place.

Referencing

If you use MS Word with the Zotero plugin, then it's pretty straightforward to create in-text citations and a bibliography. If you are a

L A T E X

user, as mentioned above, I've found the best way to set up your documents is to use a cloud storage service and the Better Bibtex plugin. This lets you automatically update the .bib file for a given folder in your Zotero library and save it on your cloud storage. This way if you use something like Overleaf, you just have to create a shared link for the .bib file in your cloud storage and then create an Overleaf project file based on the link. For google drive, you can follow the steps here.

Reuse and Attribution

Bringuier, S., Parsing research articles with a Zotero workflow, Dirac's Student, (2023). Retrieved from https://www.diracs-student.blog/2023/03/parsing-research-articles-with-zotero.html.


  @misc{Bringuier_23MAR2023,
  title        = {Parsing research articles with a Zotero workflow},
  author       = {Bringuier, Stefan},
  year         = 2023,
  month        = mar,
  url          = {https://www.diracs-student.blog/2023/03/}# 
                 {parsing-research-articles-with-zotero.html},
  note         = {Accessed: 2025-04-16},
  howpublished = {Dirac's Student [Blog]},
  }