Filing System for Research Papers

21 Feb

The Inbox Zero Google Talk recently inspired me to get my research life organized. E-mail organization was a logical place to start, and my desire to try to keep a low number of messages in my e-mail inbox was easily adaptable to the “process down to zero” method promoted by Inbox Zero.

Now I’ve moved on to research papers. For the last several years, I have collected papers in various places (PDFs in a references file, printouts all over the place). When I actually need to organize these for some reason (i.e., to write a paper), I typically go and download all the citations into either Endnote or Jabref, and then assign each paper a unique 5-digit ID number. Then, I put that ID number in the ‘label’ field in Endnote, and keep the PDFs and papers sorted by ID number in my computer and/or filing cabinet.

This system is great for finding things fast, as long as I know what I’m looking for. However, if I want a number of papers on a particular topic (let’s say, ‘synthetic biology’), I either need to do some searching within Endnote (which can be hit-or-miss), or I have to know by memory who wrote the papers on a particular topic, search for those authors in Endnote, and then retrieve the papers by their 5-digit ID number (my memory doesn’t do well at this).

In the end, I duplicate a lot of effort in finding papers that I’ve already “found”.

I’ve done a bit of googling on this topic, but nothing convincing has come up. The best resource I’ve found was at Ask Metafilter, and it’s pretty weak. Some of the possibilities I’m considering are:

  • File by category – This works well for quickly finding a set of papers on a particular topic, but it can fail when one paper belongs in multiple categories (either you won’t find it in the folder where you think it should be, or you will have multiple copies of papers in your file).
  • File by author – This has a lot of the same drawbacks as filing by ID number, but the added advantage of forcing you to think more about who writes what, and becoming more familiar with their names.
  • File everything electronically – This scares me, because I still prefer reading papers on paper. However, it would greatly simplify the storage and searching process. How bad is it for the environment if I just print a paper every time I need to see it?

If you are faced with the same problem, or a similar one, I’m curious to hear how you handle it. I know no system will work for everyone, but I’d love to try something that simplifies and streamlines the process. I’m also interested in comments about particular software or processing steps that you like.


Posted by on February 21, 2008 in Alchemy


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7 responses to “Filing System for Research Papers

  1. generic geek girl

    February 21, 2008 at 7:03 pm

    The easiest thing to do may be to set up a database into which you enter the title, authors, publication name, abstract and keywords/categories (and anything else you might like to search by). Also note where you are storing the paper, whether it’s electronically or a hardcopy. I’d recommend filing either by author’s last name, or by the unique id number provided by the table.

    You could also use a spreadsheet or even a plain text file, if you are more comfortable with those formats. I think these would be more difficult to search and cross-reference, and a database is really easy to set up. It can be as simple as one table with a single row for each paper, or multiple tables which reference each other (which helps make things more uniform, in terms of publication and author names). You could also write a frontend that inserts new publications and takes care of more complicated queries for you.

    As for printing things out as you go, it really depends on how often you would need to, whether you always need a hardcopy for what you’re doing, and how much physical space you’re willing to dedicate to papers. I definitely understand the preference though to have a printout of something if it’s long, versus reading it on the screen. If I feel I’ll need it again soon, or want it as a regular reference, I’ll hold on to it, but for the most part, I don’t feel too bad about tossing it in recycling when I’m done. Electronic storage is relatively cheap, but my apartment is pretty small 😛

  2. halfawake

    February 21, 2008 at 11:22 pm

    Thanks for the comment, ggg!

    So, as far as a database is concerned, Endnote and Jabref pretty much have that covered (Endnote is the option that works well with ms word, Jabref works well with LaTeX). These database options are great because you can almost always download citation information from the internet directly into the software. Also, they simplify the process of adding citations to a document you are writing. The records in these programs are searchable as well. Currently, I store all the papers by a 5-digit ID number (one that I generate).

    The physical space I dedicate to papers is currently about 1.5 filing cabinet drawers, and that already feels like a waste of space for papers that I rarely look at. More importantly, though, the ID number filing system isn’t great for getting a bunch of articles on a particular topic. In other words, document number 10321 may be totally unrelated to document number 10322, even though they will be physically stored together. Maybe I should start recycling the papers I use less often, and keep scanned electronic copies (just gotta find one of those super fast document scanners!)?

  3. Frank

    March 27, 2009 at 7:07 am

    A problem that I find with filing by author is that while I will often remember the research group or the professor that published the work, i find it is very difficult to remember every individual first author.

    So then you file by professor or group, but what happens when it is a collaborative effort between research groups?

    After a 2 year research masters, and a 4 year PhD I still haven’t found a solution I’m happy with. What generally happens is that I print everything, and stick it in a pile “to be filed” where it stays forever and then I thumb through the pile manually when needed. Very inefficient!

    I find now that more and more I print the paper for the first read through and then if I need to refer to a paper again and I can remember anything about it at all (keywords, any author, even a phrase from the text) then google scholar will almost always do the hard work for me. Still results in a lot of manual inputting of references when writing though.

    Now at the beginning of a postdoc I intend to get my house in order and start using some bibliography software (is there one that can link to an online copy of the paper?), along with google scholar and a filing cabinet.

    The best laid plans…..

  4. halfawake

    March 27, 2009 at 8:29 am

    “Now at the beginning of a postdoc I intend to get my house in order and start using some bibliography software (is there one that can link to an online copy of the paper?), along with google scholar and a filing cabinet.”

    Frank, I feel your pain. It doesn’t seem there is a great way to do this. I’d recommend using Jabref or Zotero… They may have some of the linking capabilities you’re looking for. Otherwise, I still don’t know of a consistently good solution.

  5. binsento

    November 17, 2009 at 11:37 pm

    Wrote an answer to this post over here:

    Any input highly appreciated.

  6. halfawake

    November 18, 2009 at 12:21 am

    Thanks for the feedback binsento!


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