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How to organize large libraries in Mendeley

Hello Everyone,
The official website of Mendeley Desktop contains detailed tutorials on how to interact with the software, which tools are available and how to use them.
For what Mendeley is for, I guess we everyone got it already: an all-in-one software that allow us to organize our library for research papers/books/etc… in a fast, easy and interactive way. Mendeley allow us to easily find research that is related to our database as well as sharing our library with collaborators and partners.
In my opinion, and now that we have the tool available (Mendeley), the great question is on how use it correctly. Said with other words, how to organize our Mendeley library in a way that it honours 3 functional rules:
  1. grow in size to infinity;
  2. grow in complexity to infinity;
  3. maintaining always easy and logic the path to find the paper we are looking for.
It is important to recall that, managing a library of 100 to 500 research articles (at the level of a Bachelor or Master Degree) is way different of managing a +3000 as is required for a PhD, Postdoc or above. The rules that may work in the first case will lead you to despair in the latter.
Nowadays, Mendeley considers two ways to organize and catalogue articles: through Folders or through Tags. I have discussed the functionality of both in other posts [1, 2, 3].
There comes the question:
How can we organize our library of research articles from the beginning of our career (starting from Bachelor, for instance) without having to face in the future situations like:
  • where is that paper that I have read so many times but now I can’t find?
  • what a mess I have here… can’t find anything I am looking for.
  • better start to organize my library… otherwise working will be impossible!
This last exclamation is much more common than what you may expect and is a good example of Procrastination. :-)
To answer our question and honour the 3 functional rules, we need to introduce two concepts in organization: linear organization and ecosystem organization. This concepts, as you will see, will be useful to organize your articles in Mendeley as well as organizing anything else in your work or daily living.
1) Linear Organization
When a student starts is research career and little by little starts to collect scientific literature, she or he will be able to easily handle the library because it won’t be larger than 200 papers approx. It is easy to remember all the papers gathered. In such situations it seems logical and straightforward to archive the articles based on a logical hierarchy of themes and topics, having them divided into folders, for example:
  • Cancer
    • Lung Cancer
  • stem cells
  • biology
    • plants
  • Proteins
    • Disordered proteins
  • Nuclear Magnetic Resonance
    • Structural Biology
    • Theory
  • etc…
At the time of searching for a paper in our library, this first level of organization restricts the search to the top most topic, selecting the subsequent folders, we restrict the topics of relevance until we find the paper we are looking for. In this way we go through the hierarchy of folders and subfolders. This kind of search and selecting is always linear and immutable.
  • Cancer -> Lung Cancer -> Mice Experiments -> Membrane Proteins
  • NMR -> Structural Biology -> Protein Folding
This system of organization, though of logic creation and easy handling, does not honour the 3 functional rules of organization because it allows only for a single starting point for searching a paper inside the library.
1. Can this system grow to infinity in size? Yes.
2. Can it grow to infinity in complexity? No! the information is always organized in a pyramidal a hierarchic fashion.
3. Will it be always logic the path to find a given paper we are looking for? No! As we will discuss shortly.
In this way, the linear system of organization results too simple and too unprofitable when facing the large complexity of the advanced academic research life that requires multidisciplinary searches in libraries above 3000 articles, to say the least.
2) The Ecosystem MethodScreenshot - 010814 - 18:21:47
Pyramidal systems are condemned to perish as they cannot stand infinite growth unless a equal infinite source of resources is available. On the other hand, it is much more sane and fruitful to adopt an ecosystem mode of functioning. This kind of organization can be achieved through the use of Tags in disregard of Folders.
In this way, to each paper we attribute tags based on the concepts addressed. By not having a pyramidal system, the search for a paper in the database can be performed starting from any point of interest and can be related to any other concept of relevance. With an ecosystem of tags we can execute the following search:
Cancer <-> Magnetic Resonance <-> Mice experiments <-> hyperpolarization.
And we will get from our database the papers that are related with such concepts. The complexity of the academic life demands flexibility at the time of searching for papers, we need to be able to look for them based on which concepts made us remember about that precise paper in that precise situation. A pyramidal hierarchy does not allow such flexibility.
No topic is more relevant than other, there is not hierarchies in sciences! The importance of each topic is given at each given situation. A research may be important because it addressed a given protein or a given technique.
An ecosystemic organization honours our 3 rules of organization.
  1. Can it grow to infinity? Yes! unless we completely fill up our hard drive :-P
  2. Can it grow in complexity? Yes, because articles are organized by concepts that can be related without any kind of hierarchy to bias the search.
  3. Will it always be logic the path to find what we are looking for? Yes! Because we can search any concept and relate it with any other.

In Conclusion:

Considering that we can use simultaneously Folders and Tags, mi suggestion is not to use Folders and stick only to tags! Your “me” from the future will thank you for a healthy ecosystem! :-)

Hence, for what folders are useful for?

In the organization of a library of scientific papers, I think that folders should be used only to separate themes different enough not to have relation between them. For instance, “scientific papers” and “bureaucracy”. Even books and papers should belong to the same folder, in this example. Another example where you can use folders (in Mendeley) is to temporarily organize articles for a given work, for example, the articles that you are going to reference in your next paper, so you can access them easily.

In fact, in the first versions of Mendeley didn’t had folders at all, it was based solely on tags. By user petitions folders were added.

Keep in touch,


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