How I organise my references and papers to read with Zotero

A short summary of how I use Zotero to track papers I read and save those which are relevant to my work (current, past or future)

Hi, there are many tutorials and videos out there on how to use Zotero but I wanted to make a quick guide on how to start using Zotero when you have used PDFs in saved folders for a long time. I like Zotero because it is really convenient to find PDFs of papers, save papers, read them, search in your library and your notes, and also cite them as references when writing.

It is especially good for my ADHD brain, so I can function as a scientist despite having a mind all over the place, woohoo! :D

Saving papers

1. Drag PDFs: When I was initially setting up Zotero, I was transitioning from a manual organisation of PDFs. The easiest way to start for me was to drag my PDFs into the app. It converts them into a book/article/whatever.
2. Zotero connector browser extension: The browser extension is the way I do it now about 99% of the time. When reading a paper online, you can click on the Zotero option, select the collection you want it to be part of and voila! It’s in your library! It also automatically finds a PDF if it is accessible and downloads it for you.
3. Import citation from a file or clipboard: So a few times you might want to import citations from text or files. For example, when you ask R for citation(), it gives you the text as well as a BibTex citation:

@Manual{,
 title = {R: A Language and Environment for Statistical Computing},
 author = {{R Core Team}},
 organization = {R Foundation for Statistical Computing},
 address = {Vienna, Austria},
 year = {2020},
 url = {https://www.R-project.org/},
 }

Or, sometimes softwares can export a text file containing similar entries. In that case, simply copy the BibTex, go to Zotero>File>Import or Import from clipboard, and Zotero will do everything else for you :)

Note: When citing websites or softwares hosted on a web server, every website has a preferred way of being cited. Zotero does not do that automatically, so it is good to check how they want to be cited and change it manually in Zotero, especially the title for the citation. Sometimes you also might need to change the author name or title for webpages. For example, my colleague has two last names but Zotero always imports one of his last names into the first name.

More info on importing, e.g. by ISBN, DOI or PMID: https://www.zotero.org/support/adding_items_to_zotero

Organising papers and searching library

1. Collections as categories: I organise my papers by their relevance to me, or relevance to the topic they are a part of, e.g. I have very specific categories for when I have many papers about something, like “phage resistance”, “phage resistance and antibiotic”, “phage therapy clinical”, but I have broad categories like “microbiome” for topics that I have few papers on. I also have “methods/softwares” as a category.
2. Make a note or extract highlights: I sometimes note down the findings of a paper and also how it is relevant to my work. For that, click on the paper>Add note. I also highlight important sentences while reading. Then I can make a second note from annotations by clicking on the paper>Add note from annotations
3. Tags: Tags can be useful too, like “review”, “new combination”, etc. I add all tags in my notes for me to use as search strings later, but you can see if you like tags better.
4. Searching papers: Sometimes you want to search every word in a paper and your notes, versus sometimes you are specifically looking for an author or paper. Zotero has various search options available by clicking the magnifiying glass on the right, like “title, creator, year” or “everything”. (Or click the magnifying glass in the middle, for advanced search)

For more about searching: https://www.zotero.org/support/searching

About ADHD-friendly: I write my thoughts about what I read in the notes, kinda like writing on the margins of pages. I also search in Zotero using the “everything” option, which is amazing because it searches even for words in PDFs. I add a particular paper/book to multiple collections so that I can find it when I am scrolling it. And if I do this process enough times, I don’t remember a paper but I will remember where it could be on Zotero and then find it, haha!

Referencing while writing reports or articles

1. Plugin: I prefer the Word plugin for MS Word. There’s also one for open office
2. Add citation: In MS word, Zotero>Add/Edit citation and that’s it! First time you open it in a doc, it will ask you to choose a style. Then you just search for the citation and it adds it!
3. Add bibliography: In MS word, Zotero>Add/Edit bibliography. That’s all!

This convenience of adding/searching/citing is why I love it. Hope it helps you in your research. K byee!! As usual, leave a comment if this helped you.

My library, examples of collections