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I'm looking for a reference manager with note-taking/quote-storing capabilities. I don't need a full knowledge management suite, but I want to find a program where I can store and search long notes/lots of quotes, attached to entries in my bibliography.

So far I've used:

  • Bib(La)TeX + pen and paper
  • Zotero
  • Mendeley
  • Paperpile
  • (Not sure about Endnote, but at least I haven't seen it used for what I need.)

Pen and paper obviously isn't searchable, and funnily enough, neither are the notes in Zotero. All of these programs treat notes as negligible, focusing on PDF metadata import and annotations, PubMed or Google Scholar search and whatnot. Which is all fine but not what I'm looking for. Since I work in the Arts & Humanities I still have my fair share of books accompanying the PDF articles in my work routine. For those I don't need any online specialties but rather a way to attach lots of quotes, notes, summaries and so on.

From what I've heard, Citavi can do some things like that, but I'm nowhere near a Windows computer to try it out. Ideally I'm looking for Linux programs, I could try Mac, and give bonus points for a web interface.

  • Unfortunately the other two programs linked in that question are very old and seem to be not maintained anymore. – Matthew R Aug 22 '16 at 19:56
  • Citavi would be my go-to option, but I think it's Windows only. You could always use it with Wine or some other virtualization tool. It's not free if you need more than a (too small for me) set of 100 references, and it has its limitations (and slow solution of them), but it works well. And they seem to be going online (cloud-based) at some point in the near future. – ASR Mar 29 '18 at 17:48
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I use BibTeX / BibLaTeX with Jabref. I make use of the Annotation Field. See this TeX.SE answer for some details on how to enable the annotation tab on all entry types.

In JabRef, the search bar allows you to search all fields, so that gives you searching. I particularly like getting search results from my annotations and from the abstracts. And you can store by each of the fields -- including the timestamp of when you added it. It also lets you easily link to the PDF and/or URL/DOI. I suggest if you can link to the URL/DOI in preference, since that will work on any computer if you transfer the entry.

To add things to Jabref is just a matter of pasting the BibTeX entry code -- or it has a number of other options.

Jabref just fronts the BibTex file, which is really nice if you need Bibtex to use latex referencing -- but I guess for most fields of humanities this is not so significant.

BibTeX is also really nice because it is just plaintext field, so you can version control it cleanly. See this Tex.SE question Even if in humanities, version controlling your referencing is a great idea, since it makes it centrally available (if you use hosting), and gives you backup, and merging.

  • Thanks for pointing out JabRef to me. I just gave it a go and the review/annotation field works just as you described. It still feels a bit like tricking it into doing what I need, though. I can only imagine how unwieldy things get once I start storing 20 pages worth of quotes for one entry in that review field. I'll keep an eye on JabRef but I'd love to find a program where quote management is a thought out feature, with a way to handle quotes individually (tagging them and so forth). – Matthew R Aug 22 '16 at 20:11
  • I hear what you are saying. A "Quote Manager" rather than a reference manager, if you like. – Lyndon White Aug 23 '16 at 7:41
  • Yes. Searching for that doesn't really yield helpful results, though. I shall keep looking. – Matthew R Aug 23 '16 at 9:16
  • Good call for using the annotation field. It is worth pointing out that this is a BibTeX feature that works independently of the reference manager that you are using. You could, for example, also write down quotations/excerpts into the annotation field using Zotero, which would then be searchable as well. – henning Mar 7 '17 at 14:53
  • @MatthewR This is what I do — I'm also humanities. Annotations in Bib(La)Tex for me is just a large set of quotes and I used the abstracts for my own personal summary of the article (since formal abstracts aren't super common for our articles). Someone could potentially extend it with a specific storage format for quotes, but it seems to work mostly for me saving quotes. I admit for anything longer than two or three sentences I tend to give the a thematic title/summary, though, and just pull out the book/PDF if necessary. – user0721090601 Mar 9 '17 at 1:19
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Even though you mention it, I think Mendeley actually solves you problems. It doesn't actually ignore notes, and you can actually search through them, so it seems like it should satisfy your needs.

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I spend most of my time working in Linux, so that colors this answer. I'm a strong believer in the Unix philosophy of "each program should do one thing and do it well".

To that end, I use Zotero to track my bibliography, but I use Microsoft OneNote (running in a Windows VM on my machine or on my laptop) to take notes.

Zotero nicely syncs across my various machines, so it's trivial to copy and paste either the title or the DOI of an article to OneNote regardless of what computer OneNote is running on (unfortunately, Zotero doesn't seem to support links directly to the Zotero entry).

I'd love to have a free/open-source notetaking program (and even better would love to have one integrated with a reference manager). But I have yet to find a single program that can track references and take notes better than the combo of these two.

  • 1
    This is similar to what I've come up with (for now). I use Zotero for the bibliography and Google Docs for note taking. One file per book/paper, named after the BibLaTeX cite key, with just a really simple template to set indentation so that I can easily see page numbers of quotes and so on. Different colored text for quotes and my thoughts. I find this works the best for me -- and while not directly linking bibliography and quotes, most importantly it is platform independent and I can access my notes everywhere. (The web interface of OneNote just isn't for me.) – Matthew R Mar 20 '17 at 13:50
  • @MatthewR - Since comments are ephemeral, why don't you post an answer? – aparente001 Mar 26 '17 at 22:38
  • Thanks, this is a great answer, it has motivated me to start using Zotero! – Penanghill Jun 19 '18 at 5:10
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To provide another answer myself, Sente for Mac does have a "Notes" tab, where you can input individual notes per reference, complete with a field for page numbers and comments.

However it was super slow on the Mac I could test it. So I'm still open for other suggestions before settling in, especially for programs where the "quotation management" takes center-stage rather than being an aside.

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I have tried Mendeley and investigated others like Papers (for Mac) or Sente. I actually came back around to Endnote for reference management, pdf annotations, and note taking. I like Endnote's integration with Microsoft Word so I can quickly insert citations and I don't have to worry much about formatting a bibliography or reference list. You mentioned a few things you're looking for: 1) storing and searching quotations and notes and 2) some pdf annotations.

  1. For note taking, or quotations, there is a field in each reference type called "Research Notes" which is used for this purpose. It won't appear in reference lists but is searchable and you can display it in Endnote easily. You can also search within your Endnote library by "Any Field + PDF Notes," "PDF," or "PDF Notes" meaning that these annotations are easily searchable. Endnote search options

  2. For note taking with Endnote I tend to prefer attaching the pdf after doing text recognition. I'm not sure if newer versions of the program do it automatically but most journal pdf downloads already recognize the text. I highlight or add comments in the pdf. (This can be done through Endnote but I prefer opening the document in Adobe Acrobat Pro by right-clicking on it.) Any OCR'd text or comments are searchable.

You mentioned the interfaces - I've used Endnote on Windows or Mac and they are identical interfaces. On Mac the Word integration was a little more difficult, though I'm not sure if recent versions have fixed it. There is a web interface, Endnote Web, that allows you to synchronize everything as well, so my libraries stay up-to-date no matter what computer I'm on. The web interface is a little slower but the research notes work just as well. The PDF attachment process requires downloading and re-uploading the pdfs and PDF text is not searchable.

  • Right now I'm on Linux only, which does considerably limit the available choices. But thanks for your detailed answer. I'll try Endnote again once I have the opportunity. – Matthew R Mar 20 '17 at 14:08

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