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I'm a researcher and so far I've been accumulating hundreds of papers, articles... The point is that I want to organize them by choosing a consistent file naming convention. This is driving me crazy.

I explain better. Let us consider, e.g., an article whose title is "An Article with an Interesting Content", by Mister Writer, published in 1999. Since I would like the names to be quite short for readability, my first guess was something like this:

"Writer-1999.pdf"

The problem with this is that I can not search among files by the articles titles. So I went for

"An_Article_with_an_Interesting_Content-Writer-1999.pdf"

which I personally find kind of cumbersome.

What do you think?

EDIT: I work on a Linux/Unix machine with LaTeX. I haven't choosen a software to manage documents yet.

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please add information about your operating system and maybe about other software you might want to use the references in for writing scientific publications (LaTeX, MS Word, LibreOffice, ...?) –  Martin Feb 6 at 13:49
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9 Answers

I think you should use a destinated software for managing your reference files. Article titles usually are quite lengthy and I (personally) would leave them out of the filename or at least only use an abbreviated version.

There are a lot of powerful solutions to manage literature and reference information. It would be very helpful to know more about your operating system and working environment to give a speficic advice.

Software for managing bibliographic data and notes

For Linux and LaTeX I'd recommend using JabRef, which can manage your Bib(La)TeX bibliography very comfortably. It's open source, platform independent and very powerful - I've used it for years. It can even manage your collection of PDFs for you, if you like that.

I'm working with a system where the PDF is only named AuthorYear, e. g. Miller2010b or Bush1989f and all other information is only contained in the bibliographic metadata in JabRef (as well as in the full text of the pdf).

For taking notes or saving excerpts of those papers, I had a large collection of text snippets, each one with a title starting with the source like "Miller2010b: reference managers are very useful"

I'd also recommend having a look at Docear which is also free and open source and extends the concept of JabRef (which is integrated in Docear) to a very powerful note taking system based on mindmaps.

Another way of taking, managing and tagging notes is e. g. Emacs orgmode, which also can work together with LaTeX or other markup languages.

other sources

I'd also recommend having a look at this site: http://www.organognosi.com/ The author built a very sophisticated system for note taking etc. in a scientific working environment. Some of the tools used there are only available for MacOS X, but the general idea might be very inspiring.

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+1 tagging and metadata is where it's at. –  Raystafarian Feb 7 at 15:09
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Caution: I've been doing this for 8+ years, so I'm pretty much committed to my way of doing things. Beware of commitment bias!

Here's my flow for your reference. I use a similar file naming scheme:

Author1_Author2_Title_JournalAbbrev_Year.pdf

I have a directory structure that group papers I read/saved for a day nested inside a rough classification:

$REFROOT$/Neuroscience/20140205_spatial_memory_task/

This allows me to quickly search files in most cases, or just browse what I have researched in the past. To search for an author I would search filenames containing "lastName_" and it lists papers with that author.

For every paper, I also use citeulike.com to save the bibliographic information, keywords/tags, and also the personal pdf's. Often times I do not have network access, and since local file system lookup is faster, I first search locally. If I need to view "all papers by author1" or "all papers tagged ABC", I use citeulike. Citeulike has 2 advantages: the smart bookmarklet can automatically extract information from journal websites or from ISBN/doi, and exporting them to BibTeX entries is a single click.

I do not use this functionality, but JabRef can add to your BibTeX file the location of your pdf. This would be similar to using Papers in Mac to organize all your papers.

These tools operate smoothly cross-platform, and I use them across Windows, Linux, and Mac OS machines.

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You need software that lets you search within the PDF text. The filename should almost be irrelevant, because you are probably more likely to remember a sentence or concept from within the paper than the exact author name. A program like Evernote can do in-document searching; in fact, your normal operating system should be able to look within most OCRed documents. Have you tested searching within document text using Finder (Mac) or Explorer (Windows)?

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Author info is important meta data that searching PDF wouldn't do. Title info is also not going to be easily accessible either. Because in the bibliography of many papers, same author names and titles will appear. –  Memming Feb 6 at 17:31
    
I've been using Finder to search among my documents. –  Davide Feb 6 at 20:10
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Using the file name as an organizational tool is not the appropriate strategy.

The appropriate strategy will focus on the ability to search your documents as others have mentioned and the ability to apply descriptive metadata.

Descriptive meta data is about layering your categorization so you can organize your documents by multiple parameters.

I would recommend for example categorizing by Author, date of publication, the Dewey Decimal system, and keywords.

The reason the file naming method is driving you crazy is because you are trying to concatenate these multiple layers of organization into one string. That makes it difficult to expand or index effectively.

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All file naming conventions suffer from the same problem: they are arbitrary and don't allow users to find the information they want quickly. With that being said I try giving my documents fairly descriptive names while at the same time trying to keep them short.

I think Google Docs would solve the problem you are experiencing. I keep all of my digital resources in Google Docs for the following reasons.

  • Search-ability. Google arguably provides the best free search engine on earth. Not just searching by title but the document's content as well.
  • Cost. Free - nuff said.
  • Complete solution. Nearly all my documents are completely text based. Converting them into Google Doc format (Google's native document format) allows me to store an unlimited number of documents. Store ALL of my documents here.

Additionally, I can also access all of my docs from any device.

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+1 for the suggestion with mostly text based documents - I just want to add, that each one has to consider for himself if it is a good idea to store all or part of his private (or even business) information at a company like Google... –  Martin Feb 7 at 8:08
    
Google is THE FIRST company to post a transparency report detailing all personal information (to the maximum extent allowable under law) that has been lawfully required for Google to give to public officials (started in 2009): google.com/transparencyreport –  Aaron Klap Feb 10 at 22:33
    
Google values people's private information and strives to keep it private more than any other IT business in existence today. Google was built from the ground up as an information storer and provider. Google has turned information handling into an art-from and has been so successful at collecting information because it lives and breaths transparency. Google has released open-source keys through APIs for ALL products that they have made and is the largest company in existence that has ever done so. This opens the company up to extreme scrutiny at an unprecedented level. –  Aaron Klap Feb 10 at 22:36
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Have a look at citeUlike. You can keep all your research material in your own library, with excellent organization.

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I'd put the Author as a folder on it's own. I'd drop the Year, unless it's absolutely necessary or convenient, where it'd go in a subfolder. Combined with long file names, the last bits would get hidden. I'd keep the full name of the article but use spaces instead of underscores for readibility. I'm not sure if your file system supports this but it hasn't caused me any issues with Ubuntu or Windows.

So, it'd be: /Documents/Writer/An Article with an Interesting Content.pdf

or /Documents/Writer/1999/An Article with an Interesting Content.pdf

or even /Documents/Writer/1999 - An Article with an Interesting Content.pdf

The last recommendation puts the year at the front so that it doesn't get hidden. You can always choose to drop years or put them all in the same folder. Windows allows you to search for file names (not sure about Linux), so it doesn't matter if you're hiding all your documents under an author's name.

Multiple authors may be an issue. Just pick one folder for the best known author in the field or put them without a folder.

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My programming teacher in college stresses over these in our assignments.

The one he recommends and that I also like is camel case. It looks like this: thisIsMyFile.fileExtension . You can apply this to almost anything you name.

Also keep the plural versions out. Instead of using a file called: myPictures , use myPicture .

From what I can tell this improves readability and looks nice when searching through many files.

I hope I was able to help you out somewhat with my answer!

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For mac I recommend something from ironic software called Leap. Basically you just tag it. Then you throw it in a magic box and forget about it. And you get a nice tag cloud to navigate for things.

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This seems like it might be promising, but expanding your answer with some links or examples would really allow users to get a clear picture of why you've recommended it. –  Raystafarian Feb 7 at 15:10
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