How do you manage your literature and references?

Question

I have many PDFs (articles, reports and other literature) in various folders, and most of them are also in Endnote, which I have always used as a reference manager. However, the references in Endnote are not linked to the PDFs (most of the references were downloaded from journals' pages, but Endnote can find the PDFs for only ~30% of the references I have in there) and I do not have any 'tag' for the papers. My plan to fix and have a more organized library is the following:

• Re-download references directly from journals (hoping that Endnote this time might find the PDFs for these)
• Link remaining PDFs manually, putting all PDFs (including the ones from the point above) in one folder
• Link PDFs to NVivo, so to add different tags to the same article and to search more easily through the literature

However, this manual process seems to me very slow and easily prone to mistakes. Therefore, a few questions:

• Can this process be automated somehow? Looking into the future, how do you go with downloading individual PDF and references and keeping the literature tidy?
• Are there other options for having all PDFs in one folder (possibly with file names corresponding to "author year title"), linked to a reference management software (Mendeley, Endnote, or Zotero?), linked to NVivo?
• More in general, how do you manage your literature?

Thank you very much in advance!

Answer 1

I have approximately 15K PDF documents organized roughly according to Universal Decimal Classification (UDC) in about 2.8K folders. I synchronize these files across a couple different computers with rsync. I use UDC to get some basic organization and have many improvements and additions to the classification as I find UDC to have gaps and be illogical in many parts.

I also use Zotero to manage citation data for the documents, though the folders and Zotero are not directly linked. The files are named consistent with the citation keys in Zotero, so, for instance, if I know an article has the citation key citation_key in Zotero, I know to look for citation_key.pdf in the folders. I have some helper scripts to automatically open a PDF file or its folder given its citation key.

The folder approach has many advantages:

• Much faster than citation managers or search engines.
• Future-proof. Presumably computers will have some sort of hierarchical file system in the future. (Also see below about losing journal access being a reason to keep PDFs.)
• Uses the existing file system, which means no additional software is required. This also means there is no vendor lock-in. And you can use a wide variety of existing software to do local search, for example, using the native search tools, Everything, or Recoll.
• I can get hyperspecific on the topic. To give an example, dimensional analysis is an interest of mine. Most classifications might have only one subdivision for the subject. I have about 150.
• I personally find that organizing documents helps improve my understanding of a subject. It often takes a fair amount of knowledge to know how to categorize something.
• When compared against tagging, using a folder hierarchy is basically "tags with inheritance". This makes getting very precise easy as you can simply place a file deep in the hierarchy. To do the the same with tags, you'd have to apply more tags, which usually takes longer in my experience with software that uses tags.

A common argument against a hierarchy is many documents or parts of the hierarchy should appear in multiple parts of the hierarchy. I get around that with shortcuts/symlinks/whatever your computer calls them. I have about 3.3K symlinks at the moment. Yes, this is not ideal, but in practice it works fine.

My approach works for me, and I know from r/datacurator that I'm not alone. Many people disagree with this approach, and that's fine. Different approaches work for different people. With that being said, I want to respond to Louic's answer:

libraries of literature already exist on the internet

Why should one be limited by what's online? There are gaps and flaws in any database, and there are many documents that have never appeared online. My own personal collection fills in these gaps and corrects the flaws in my field and is a competitive advantage I have over others.

Also, your journal access may change in the future. Keeping copies of papers ensures that you don't have to figure out how to get them later if your journal access changes.

search engines are good if you know how to use them

As I've said, all databases have gaps.

Also, don't overestimate human search abilities and memory. There have been many times where I remembered that an article existed on a particular topic, but I couldn't find the article easily or at all.

And academic search engines today focus heavily on text search. I know from my experience searching patents that classification search is essential to get around the problem of unknown synonyms in text search. For more esoteric topics like those studied by academics, I haven't found semantic search engines like Google Scholar to consistently understand what's a synonym, so that's not a replacement. One way to do classification search is to make the classification yourself, as I do. (Another disadvantage of text search is information that doesn't appear in the text or is difficult to find with text search. This includes information in figures and anything that requires some sort of analysis to determine.)

your library will quickly become too large to manage (unless you want to become a full-time librarian)

This is merely an assumption. In my experience, 15K documents are manageable with a reasonable organization scheme. (The organization scheme doesn't need to be folders. I think tags could work great too!) I believe I could handle an order-of-magnitude more documents without much trouble. I see many others put everything in one giant folder or search online to get papers again, but to me either approach is unmanageable. I couldn't manage a couple hundred documents in one big folder.

The time spent organizing the documents is not that large and pays off in the long run, I think. I work a full-time non-research job and I completely reorganized my document collection late last year on my own time. (That was when I switched to UDC.)

both your interests and the relevancy of the articles in your library will probably change over time, leaving you with a big pile of articles you will never read again

Yes, there are many documents I have saved that I may never look at again. It doesn't cost me much to keep those documents. As stated, one's interests might change, but that's not necessarily an argument for not saving documents. If I've already done the work to carefully classify the papers, I might as well keep them in case they end up being valuable in the future. My interests don't change randomly, and I am far more likely to become more interested in something I have experience with than some random topic unrelated to anything I've done. Quite a few times I had a small amount of interest in a topic at one point, but this interest grew a lot, and I valued the documents I had saved already on that topic. Many of those documents I might not have found again, or I might not have made a connection that would have led me to classify the document how I did the first time.

being well organised often means knowing what NOT to keep: hoarding papers is the opposite of organising a well-curated library

I don't save documents indiscriminately and don't recommend doing so. Some documents are more important than others, yes, and I highlight those with README files.

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I wrote more details about my system at r/datacurator.

Answer 2

To answer your general question "How do you organise your literature?": I don't. I let websites such as web of science, scopus, medline and google scholar do that for me. It may not work for everyone, but I think it is worth seriously considering this option.

I only manage a "private library" of references while writing a review or article, and this library contains only the papers relevant for the publication. I found this to be sufficient: the useful references will be listed in the bibliography of the publication.

Other reasons not to manage your own library:

• libraries of literature already exist on the internet
• search engines are good if you know how to use them
• your library will quickly become too large to manage (unless you want to become a full-time librarian)
• both your interests and the relevancy of the articles in your library will probably change over time, leaving you with a big pile of articles you will never read again
• being well organised often means knowing what NOT to keep: hoarding papers is the opposite of organising a well-curated library

To put it bluntly: don't waste your time trying to get the perfect library. Not only is this nearly impossible, but there is probably no need.

I realise that there are exceptions, and that certain fields need extensive literature libraries, and that certain universities may not have easy access to online publications. This answer is not intended for those exceptions.

Answer 3

This may be an overkill for the case, but after >15 years in academia and many organization systems, ranging from fully manual folder structures to mediocre automation system based on citation managers, as well as committing to software that stopped being developed (I’m looking at you Sente), I’ve found that the most productive and useful system for me is to use DevonThink Pro as my main database of PDFs. DT allows tagging, notes, custom metadata (like proper citation info), full-internal PDF search, and operates like a GUI file explorer. I then use Bookends (though you could use any reference/citation software for this part) for specific project/paper bibliography lists, so that I can scan my working document for citation bangs and generate a properly formatted reference lists and in-line citations, depending on the necessary correct citation format.

I find that, at least for me, this works WAY better than having a meta-library (in whatever reference software - and I’ve tried them all) of every reference (with or without attached PDFs) I’ve ever come across and found interesting or relevant, with sub-libraries for individual projects.

However, the caveat is that I use MacOS for these tools and it is hyper-specific to my needs, which involve being able to search within >30,000 PDFs (some academic, some archival) for relevant information on the one hand, and then having a very specific list of actually cited documents, with correct citation data, for unique/project or paper-specific reference lists, on the other. Just my two cents based on experience.

Answer 4

What you are trying to do makes a lot of sense, but in practice, it might be quite difficult to achieve. I will try to give a high-level explanation as to why I think so.

The key issue is tha any software that manages PDFs must maintain control over the exact file location, including the file name. This does not mean that they must dictate in which folder you place their files (on the contrary, most will let you specify a root folder of your choice), but they must be able to control the precise names of the files. Suppose, for example, that NVivo is trying to track the same exact PDF files as EndNote. Well, if NVivo changes any file name, then EndNote completely loses these files, resulting in broken file links in EndNote. And vice versa: if EndNote changes any file names, then NVivo loses these files. Thus, unless one software is integrally synchronized with another such that it is aware when the other changes any file name and then can automatically update its own records, two software systems cannot share the exact same PDF files. This is a simple restriction, but it is rather definitive--because of this, shared PDF folders are not very feasible.

Although I doubt what you would like could work, I can suggest an alternative workflow as a second-best option. You could consider EndNote as the primary manager of all your documents, so it would be the default and definitive database of all your files. (You would need to manually attach many PDFs as you described in your question.) Presumably, you do not work on all your documents during a literature review project. Perhaps you have 1000 documents total, but work on up to 100 or 200 in one literature review project. Then you would need to import (copy) those 100 to 200 documents into NVivo, and then take advantage of its features to do the in-depth literature analysis.

I know that this solution involves duplicating many articles (in my example, 100 to 200), but I do not see a way around it. I use different software from you (I use Zotero instead of EndNote and Excel instead of NVivo), but when I have such needs, I duplicate my PDFs in this kind of way.

Answer 5

I have been using Mendeley computer app for a long time now (which you have mentioned, so I am not sure this is a valid answer, but it seems to me that this might be a under-used tool in your case). It allows you to organize your pdf files in a customized folder (i.e. you import it and then it is copied to a custom folder with a custom name just as you mentioned such as author_year -- you must configure these features of course). When you do a search it shows not only the titles, but also the body content with the search you performed.

Additionally, it has a bunch of features that are suitable (for me at least): you can configure it to generate bib files with your references (in a single huge bib or individual bibs -- which is important for LaTeX users); you can confirm the article's information using its doi for instance (I find this extremely helpful, especially with older pdfs that are not automatically recognized because they have been scanned instead of created digitally); you can synchronize it with all the computers that you use Mendeley and even access your account online if you don't have it installed.

I highly recommend it! This has been an amazing tool for me.