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