how do you take & organize reading notes?

I’d appreciate your dropping comments if you have thoughts, suggestions or links relevant to good strategies for taking and organizing your “literature” notes.  I’m working with my advisees on this, and I have to say that my own procedures have been ad hoc and often unsatisfactory.  I have the index card  files from my notes taken in the 1970s that are useless now.   I (as many) have tended to do ad hoc literature reviews for particular papers, but find that I have failed to keep or organize good notes that I can return to for a subsequent project, so I either rely on the lit review from the past proposal/paper I wrote, or have to start over.  I often will remember something I’ve read but not be able to remember the citation or enough information to find it again.  I have zillions of poorly-organized photocopies made in the 1980s and zillions of poorly-organized PDFs saved since the mid-1990s.  So I thought I’d put this out to the scatterbrains to see if you have good suggestions, ideas.  We’re talking meta-suggestions for how to think about the problem, as well as tools or techniques.  It’s how to get the work done now for this project plus how to be able to access the work again three years or ten years from now.

Author: olderwoman

I'm a sociology professor but not only a sociology professor. I keep my name out of this blog because I don't want my name associated with it in a Google search. Although I never write anything in a public forum like a blog that I'd be ashamed to have associated with my name (and you shouldn't either), it is illegal for me to use my position as a public employee to advance my religious or political views, and the pseudonym helps to preserve the distinction between my public and private identities. The pseudonym also helps to protect the people I may write about in describing public or semi-public events I've been involved with. You can read about my academic work on my academic blog --Pam Oliver

32 thoughts on “how do you take & organize reading notes?”

  1. “I have zillions of poorly-organized photocopies made in the 1980s and zillions of poorly-organized PDFs saved since the mid-1990s.”

    You are not alone. Great idea for a post; I look forward to the insights of the scatterbrain community.

    Liked by 1 person

  2. I don’t have this fully figured out either, but I do have some suggestions.

    I use EndNote for keeping track of my references. For grad students out there, start early with such a program. For others, look into whether you have the resources to hire someone to help organize your materials. (At the end of grad school, I hired someone to do this for me and since then have been adding materials myself. I can’t imagine research without it.)

    In EndNote, if I feel that the title doesn’t capture some of the main points then I add keywords. It’s also easy to import/add the full abstract of a piece. Then all of this is searchable.

    For books, one possibility is LibraryThing that helps connect to others with similar libraries. There I use tags to identify books by topic, but overall I don’t use this tool that much.

    For online documents, I use the social bookmarking site There, again, I add tags and notes on occasion. The tags, in particular, help me find material later. It’s possible to have post your links to your blog automatically every day, which is a nice backup method for all this material.

    I haven’t figured out the whole organization of pdf documents on my hard drive yet. I have folders with topic areas, but of course some things overlap in which case the old-style folder format is limited.

    At some point I used CiteULike, but haven’t in a while. That one has potential as well (especially for finding related material, although I realize that wasn’t really your question).

    This year, a colleague and I have a grant to do a big lit review on a topic so we were able to hire someone for that task. In addition to maintaining an EndNote file with all of the references, our research associate has also been reading and taking notes on each paper. The notes go into a spreadsheet with specific fields. We then proceeded to hire a programmer to create a Web-based search engine for the data base. It’s quite cool. Not only does it search all of the papers, but it’s easy to click on, say, an item in the Variables field and then get a link to all other papers that include that particular variable. This tool is going to make writing the final paper much easier.

    When working with research assistants on literature reviews, I give them a grid to fill out. The grid includes cells such as data/methods, hypothesis/questions, key variables, findings, limitations. We then use this once we start writing the paper. But I’ve rarely tried to go back to this and it’s not nearly as searchable as some of the other options mentioned above.


  3. I have used EndNote before and found it acceptable. I usually use BibDesk, which is useful if your students are planning on learning or using LaTeX at all. I also use a combination of (cited above) for collecting online links and Zotero, which is a Firefox extension that a builds research database into the browser and can interface with most major collections. It’s quite nice and automated.

    I also use good old pen-and-paper, limiting myself to one page for any book or article, then I type that up and stick it on my laptop. Then, when I search my hard drive using Spotlight (for Macs), it will appear when relevant. I have a fairly organized directory structure for PDFs and a file folder structure that mimics the directory for paper copies.

    I’m still working out the kinks (I’m at the end of my second year in my program) but this worked for me in a previous MA program and is working for me here. The key is searchability and keywords. It’s also key to develop a system early on rather than trying to go through backlogs. Finding what works for you personally is the toughest part.


  4. I pretty much do the same things. I spent quite a bit of last semester putting all my articles into Endnote, including the abstract, my notes on the article, a link to the article’s online home, and the article itself attached as a PDF. Since Endnote is searchable, this works well for retrieving stuff based on vague ideas or possible keywords.

    I also group my Endnote citations according to which article/manuscript/paper I’ve cited them in, since that’s how I typically remember it.

    Then I have a single file folder of ALL my articles, with the exact same format for the title format of Name_Year.

    And the social bookmarking sites are great for online sources. I tried Zotero, but didn’t like that it was only on my laptop.

    I’ve also heard of people starting a special Gmail account that they use to save stuff to–especially when they’re away from their typical computers.

    I’ve also heard good things about Devon Technologies, but seeing as how I don’t have a Mac, I can’t use them.

    OOOH! You know what might be cool? A private blog to post your notes to! You could embed a special search engine to search your notes, and you could make your titles be the reference. You could even link to the referenced item if it is online.


  5. I write up 1-page precis of an article I’ve read. Citation, abstract, findings, some notes of my own. I post most of these to my blog, but I have them organized by subject in my My Documents.

    Can anyone tell me what’s better, Endnote or Zotero? Is it either/or, or is it more productive to use both?


  6. With respect to technology and in honor of my index cards, I should mention the large number of data tapes and floppy disks produced in the 1980s that can no longer be read. Remember to plan for the future and not being too dependent on any one technology solution. Paper backups or ASCII file exports for the stuff that cannot be retrieved again from a library are probably important. (My old index cards are actually more useful now than the stuff on old floppies.) And remember in your planning that you will probably not always be where you are now, especially if you are now youngish.


  7. Can anyone tell me what’s better, Endnote or Zotero? Is it either/or, or is it more productive to use both?

    I’d like to second this question and add RefWorks to the question as well.


  8. I use EndNote for citations, but OneNote for notes on my readings. OneNote is a hidden gem of organizational software for reading & writing ( I use a tablet, but most of the time, I’m using OneNote with the keyboard, pasting in abstracts, text, & figures from webpages (e.g., passages from JSTOR, google books, National Academies Press).

    All content – even images(!) – are searchable for text. If you have a tablet, it will search your writing remarkably well.

    OneNote uses a notebook metaphor, with multiple notebooks holding multiple sections each with multiple pages and sub-pages. Each individual page is limitless (well, limited by the size of your hard drive).


  9. I have tried many software combinations to deal with the challenges of organizing articles, taking notes, and managing citations.

    I am moderately happy with two elements of my current system:
    1. As I search for articles, I download all PDFs into one folder with standard filename format LAST NAME OF FIRST AUTHOR, YEAR, FULL NAME OF ARTICLE EVEN IF IT IS VERY LONG. Every few months I OCR all recent PDFs using Acrobat so that the minority of files lacking embedded text can also be searched. I regularly search for key terms in my large PDF library using Copernic Desktop Search (but other programs would probably work as well for this purpose).
    2. I have a large master Endnote library and when working on a paper, I connect to Web of Science and download citation info for any new articles I want to reference.

    I have experimented with Zotero and Onenote. Zotero is elegant and seems to be progressing quickly. The Zotero team is innovating much faster than the Endnote team. However, Endnote is extremely stable, which is of paramount importance. Last I checked, Zotero couldn’t handle importing the thousands of references in my Endnote library. If you access JSTOR with Zotero, you can select articles from a search query and have Zotero automatically download both the citations and the associated PDFs. Very slick! I think Endnote 12 will do this too. However, these programs have their own quirky way of storing PDFs and I really value putting all my PDFs in one master folder, which is convenient for browsing and backup.

    Onenote is attractive and convenient for storing notes but it does not integrate with Endnote or Zotero.

    Zotero is promising but for my needs, the combination of a big PDF folder and a large Endnote library works best for storing articles and bibliographic info. I don’t really have a satisfactory notetaking system yet. Theoretically, it might be nice to have notes attached to the relevant PDFs but I don’t think there is an elegant way to do this. Zotero has a note taking system but it is not easy to browse through multiple notes since they are organized like separate post-it notes, generally linked to a citation.


  10. Funny, most of the replies so far seem like (good) answers to the question “How do you keep track of bibliographical references” or “How to you store links and stuff that you might need later” rather than the original question about one’s reading notes. One promising Mac app in this vein is Papers, whose main limitation is (as its name suggests) its orientation toward articles rather than books.

    In general I feel like I do much better keeping track of references and PDFs than I do managing (or even generating) reading notes. As has been mentioned, wWhatever system you use for your notes, good plain-text export is absolutely necessary for future-proofing. Better, just keep them in plain-text to begin with, maybe using a lightweight markup system like Markdown or Textile.


  11. I feel your pain. I have morphed all my bibliographies into one big BibTeX file, which has the one advantage of being plain-text in format so being relatively immune from planned obsolescence. I use BibTeX’s annote={} field to enter both substantive notes on the item and ideas for its use in classes, future projects, etc. BibTeX of course integrates seamlessly into LaTeX, which is what I prefer to use; its integration into other packages (Word,, etc.) is less impressive but manageable.

    An example entry in my master.bib file:
    author={Jeffrey J. Sallaz},
    title={Deep Plays: A Comparative Ethnography of Gambling Contests in Two Post-Colonies},
    annote={Theoretically rich ethnographic work, suitable perhaps for 250 or 700}


  12. @10.kieran: good point! I do put long reading notes in my annote fields. I also just got a new laptop that has a tablet screen (a Thinkpad X61) which lets me “annotate” PDFs by writing in the margins, so I’ve been saving these annotated PDFs in a generally similar (although less organized) way to @9.conradhackett.


  13. One program that was designed to offer bibliographic management with a more robust notetaking system than Endnote is Scholar’s Aid ( I would be interested to know whether anyone has had a positive experience with this software. I think I gave up on it when I realized that it didn’t have as many database connection options or journal bibliography formats as Endnote.

    Like Andrew, I have a tablet. Theoretically, it would make sense to read articles on screen and do on screen PDF annotation. To be honest, I tend to just print out articles, mark them up on paper, enter relevant notes, lose track of the hard copies, and often reprint the articles next time I need them. I know this is not very environmentally responsible or efficient. But it is quicker for me to print out a PDF than to hunt for an old hard copy and more satisfying to mark up paper than to take notes on screen.


  14. @5.belle: I think that each is good at different things (I know, really helpful, right!?) Each has their own benefits and drawbacks, and as Kieran has noted in a separate (but related) context, “in the end it’s not really about the software” its really about coming up with a system that works (even as he mentions, legal pads)! Having said that, here is my impression of using Refworks and Zotero extensively and having moderate knowledge of EndNote.

    Of these three, I find Zotero the most user-friendly and intuitive. I like the fact that reading notes (to answer the original question) can be tagged in addition to the articles themselves. This means that I can tag notes that I might use for a particular paper and makes them easy to find. On the down side, it is still in development and this leads to instabilities, particularly in its integration into word processing software. The obvious downside is that it rests on a single computer (though, according to Zotero’s development roadmap, this may be ending soon.

    The primary advantage of Refworks is that it is available online. I find it difficult to use it for notes, it is difficult to tag or categorize citations and it has a very awkward integration into Word and other word processing software. Also, if you receive your subscription through your university, you may lose it if and when you leave that university.

    I find EndNote very frustrating to use. I don’t find its layout very intuitive and seems to me difficult to associate different articles with each other. It does have the best integration with word processing software. But, as I said before, I have very little experience with EndNote.

    Two other tools that have not been mentioned for taking notes that might be worthwhile are Google Docs and Google Notebook. Google Docs are nice, particularly for taking notes on papers where you might be collaborating with authors because it keeps track of your changes and allows you to share documents and edit simultaneously. Google Notebook allows you to set up an unlimited number of notebooks – and jot things down from inside your browser.


  15. Impressive answers. One of my favorite tools — in my admin job as well as this sort of work — is google desktop. Download it for free, use it, love it as I do.
    It may be the same as Spotlight, mentioned @3 by trey1.


  16. I use bookends for citations and notes attached to document, along with attaching the pdf to the citation. For general searching, I use devonthink pro. I am somewhat surprised that no one uses things like supercard or Zettlekasten. I know a few larger projects that use things like


  17. >Conrad “To be honest, I tend to just print out articles, mark them up on paper, enter relevant notes, lose track of the hard copies, and often reprint the articles next time I need them”

    I do the same – though I try and transfer the marks on the papers to the bibliographic program I use (I use Bookends because I’m on a mac, and I think at the time I bought it, it was much cheaper than endnote).


  18. Of course we are all in trouble when the oil runs out and are laptops are useless. Olderwomen, with her index cards, will be laughing at us then.


  19. @ 13 and 17: Thank you for helping me feel a bit less like an unorganized mess. I have seldom typed notes since studying for comps. I’m much more of a write in the margins and/or write down my thoughts on paper kind of girl.


  20. I tried to have a student organize my EndNote file for me at one point, but we ran into the problem that only one user is allowed to access an EndNote file. Anybody else know about this?


  21. I’m a huge proponent of Endnote – I download citation info directly from JSTOR, the university library (books), Sociological Abstracts, etc. I also take notes directly in the program (making them searchable), and set up separate libraries for each project (maintaining a single huge database that all the separate ones feed into). Only one user is allowed to access and EndNote file at a time, but you can email them back and forth as .enl attachments. AND, if one person updates the document with new citations, all the 2nd (or 3rd etc) person has to do is click on “import traveling library.” and voila, your library is updated.

    I am also a big user/proponent of Google Notebooks for grabbing and organizing online snippets that are useful – what’s nice about it is that it doesn’t make you bookmark the whole page (like de.lic.ious) but allows you to clip out the sentence(s) that are useful for you. And then it links to the whole page, as well.

    I am interested to hear more about OneNote, maybe my next big addition….

    Liked by 1 person

  22. Are any of the EndNote fans here Mac users? Mac users of EndNote reported terrible problems – including slowing down the entire machine. This was an earlier version. Maybe things have gotten better?


  23. I wouldn’t say I’m an EndNote fan, but I do use it on my Mac and haven’t had any problems. I swore last summer that I wouldn’t upgrade to the newest version just to be able to add more columns to the display, but my school had a deal so I bit the bullet. I like the ability to organize references using groups with this version (X1), though other Mac bibliography programs like Bookends and Sente do this more elegantly.

    As for notetaking and reading, I followed the excellent advice on The History Enthusiast about creating a notes template and this has proved really useful. (Also see that post for great tips on reading more efficiently – tip #1: “Read three book reviews off JSTOR to gain a sense of how this work fits into established theoretical frameworks, etc….”)


    1. Jim,

      WordPress tells me I need to be invited by The History Enthusiast to read the post. Could you possibly send me their contact info? I’m eager to hear more about this “notes template.” If you don’t have the contact info could you possibly email the text from the post on notetaking and reading to me at That would be much appreciated.

      ~ Matthew


      1. Matthew, these posts were put up in 2008. Jim Gibbon comes up readily in a Google search if you add sociology to the search string. I also cannot access History Enthusiast blog, so I think it was closed in the intervening 8 years.


  24. Just adding my 2 cents – I would recommend Zotero. It is very stable and versatile and i have not second thoughts about switching to it from EndNote. It is also easy to migrate from EndNote to Zotero and the latter doesn’t cost you something like $100 or $150.

    I also tried RefWorks a couple of years about and found it rather inconvenient and not as developed in terms of feature. I think RefWorks also costs money, but our institution had a subscription.

    So, Zotero would be my choice :)


  25. Questions for Dima and other Zotero users:
    1. How large are the Endnote libraries you transferred?
    2. How large is your current Zotero library?
    3. If you have a large Zotero library, how much does it slow down Firefox?
    4. Do you use Zotero’s PDF download feature and if so, do you have a convenient way to access those PDFs outside the Zotero interface?

    Although Zotero’s price can’t be beat, $100 would be a small price to pay for great bibiography and notetaking software. I don’t think there is a perfect solution yet but for many of us, Endnote is worth the expense. Zotero is well suited to short term projects involving no more than a few hundred sources. Its integration with the web browser is extremely compatible with modern research methods (raise your hand if you get mad when an old journal article is only available in the library). But I wonder whether Zotero is or ever will be suitable for a very large master library.

    Zotero’s dependence on Firefox could be a long term liability. Who knows what web browser you will want to use in 5 or 10 years? Firefox 3 crashes so much on my laptop that I am using Explorer until I either figure out the problem or revert back to version 2.

    Don’t get me wrong–I like Zotero and think it is an exciting product. The people working on it now seem to be doing an incredible job with whatever grant funding they have. If I ran the company behind Endnote, I would devote big money to buying out their key staff. Suppose that the lead developer does move on to greener pastures or their grant funding dries up–how portable would your Zotero library be? If Zotero isn’t updated for Firefox 4, will you keep using Firefox 3 indefinitely? I know there is export functionality in Zotero but I wonder how smoothly it works, particularly for less common materials (such as citations for conference papers) and whether there would be a way to transfer PDF links.

    In my opinion, a scholar’s bibliographic database is worth many times more than the cost of any bibliographic software so it is important to make sure that this valuable resource is stable, backed up, has lots of room to grow and is as future-proof as possible.


  26. Thanks for this post and conversation in the comments–I’m picking up some great tips.

    Does anyone use Amazon’s Kindle for reading journal articles? I’m a graduate student who spends a fair amount of time on public transportation and am hoping it might be a good way to reduce my printing and be able to use the commute time to get some reading done. Any thoughts or advice?


  27. also, I was able to download Endnote for FREE from my university library’s website. Other schools might have similar software setups.


  28. One more thing. Lately I’ve come across tips on using qualitative coding software such as Atlas.ti and NVivo to manage lit reviews. This is intuitively appealing to me, though I haven’t tried it yet b/c I’m still learning NVivo.

    Besides allowing you to do extensive coding of your notes or the text of scanned articles and books, you can run queries based on text, codes, literature attributes (e.g, year, methodology, journal), etc., and create links to other sources and memos as with a wiki. This means you could also easily link a quotation from an interview transcript with a section of an article.

    Of course if you’re not already using these or other similar programs, it’s probably not worth the time to learn them just for this. But chances are many qualitative researchers already have the skills.


  29. Bibliographic info, I’m Endnote all the way, and, like others, I keep one massive file with Author Date Title.pdf. Then I keep a series of folders for articles I’ve downloaded and haven’t yet worked my Endnote mojo on (adding online link, linking to pdf, correcting the capitalization and spelling, etc). I still end up using Spotlight on my Mac a lot, because, invariably I’ve forgotten the author or title by the time I need it again. But maybe that’s just me.

    I would love–love!–a better solution to my own notes on articles and books. I’ve been filing away hard copies with my notes on them, but that’s just plain annoying. I’m revising a piece I haven’t touched in a year, and am finding that I’m having to reread everything. (Everything. Shudder.) There has got to be a better way…


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