Miguel Panao | Professor and Author

Finding ways to improve scientific writing and academic productivity.

Organizing papers: how times have changed

To me, the amazing thing about the introduction of the iPod by Steve Jobs in 2001 was the expression a “1000 songs in your pocket.” This idea was truly a digital revolution. Therefore, for all those who are knowledge workers and do research recognize how – today – we can say the same thing about papers in our library. You can fit your entire digital library (books and papers) in your pocket. But the question is: how about organizing papers? That’s where apps come in.

Organizing papers today

Once in a conference in Heidelberg, I helped a colleague by carrying her briefcase full of papers. I understood her need because having papers we consult all the time at hand while developing ideas in a stimulating environment like a conference is a good reason. But for the next 10-15 days, my back hurt like hell!

Also, several times while developing a particular work, I remembered an expression from an article, but wondered, which one? Or wanted to look again at that paper, but… left it at home. Thus, when finally our universities adhered to a project where our digital library of articles would significantly increase, I was particularly happy with the initiative.

The next challenge was to organize papers. My organization was primary by putting PDF articles into folders according to their Journal, and all those folders into one named “Journals.” Basic. Yes. And not the most efficient way.

This possibility meant that after the digital revolution in scientific papers, like what happened to music, we needed tools in the form of apps. Today I’d like to share some of my experience and thoughts about organizing papers through some apps.


Tools for organizing papers

My experience in organizing papers started with the need to join all my references in a BibTeX file to use in LaTeX, where I write most of my scientific papers. I was using Windows, and the best tool was JabRef. It is an easy to use open source bibliography reference manager. It works like a database for papers and allows exporting them correctly into a nicely formatted BibTeX file. Thus, the organizing capabilities are limited.

Today, JabRef evolved and can directly import references from the web, and even download the papers if you have institutional access to them, but still, it is not prone to organizing papers.


Apps for organizing papers

Fulfilling the need to organize papers is where two apps proved to be resourceful: Papers and Mendeley.

The Papers App is meant to be a personal library of your articles and it is the app I use the most. You can manage your references and organize them by collections. There are integrations with other apps for writing scientific papers like Manuscripts, and it can export your references in LaTeX format.

You may manually introduce the information of an article, but the “match” feature does it for you. Searching across multiple platforms like PubMed, Scopus, arXiv and Google Scholar, you simply match the paper with the information. You can make annotations in the article’s PDF file and synchronize across platforms (mobile and desktop).

The problem is its restriction to the macOS/iOS ecosystem, and the price. If you want to consider it for Windows, developers recommend its sister app readcube.

In the sense of a more cross-platform app, you have Mendeley. It is free, although you may subscribe for a Premium option with further support. Its functionalities are similar to Papers. The only reason I don’t use it more is the design which I found less user-friendly, but given the price advantage, you may want to try this app instead of Papers.


The logic behind organizing papers

With a tool to organize papers, how will you do it? The first basic approach, which JabRef uses, is chronological. However, it misses the context of your papers. You may work with different topics and organize your papers chronologically mixes research topics. Thus, you can lose yourself unless you’re good with dates.

The natural approach would be to organize papers by topics. In the Papers App, we can do it through “Collections.” However, when you use these Apps, you’re probably writing a paper, right? Therefore, I wonder if a good way would be to organize by “Topics” and “MyArticles,” which is an approach I’ll try in the next few months.

Question: what’s your strategy for organizing papers? What is the best tool you use to do it? You can share your experience in the comments section below.

About Miguel Panao

I am a Professor at the University of Coimbra in Mechanical Engineering. I am also author of books in the fields of environmental ethics and Science and Religion. From the several research projects, this site is personal and dedicated to the search for the best approaches, tools, techniques to improve scientific productivity.

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