So when writing a manuscript I usually go about as follows: When reading papers on my topic I copy/paste or summarise those parts, which may be relevant for me and collect all these bits in a Word Document. It'll look like this:

Species A grew taller than Species B (Smith et al. 2013)

Growth rate depends on genetics (Miller et al. 2012)

For Species A growth rate did not differ between experiments (Jones et al. 2013)

So basically a list of statements that I then regroup (manually) by topic. However, that last part is quite tedious (and I have to decide on how to group the bits, e.g. by "Species A" or by "growth rate").

So I am looking for a tool (online or downloadable) with which it's possible to collect those text bits, assign tags to each and then select which tag to group by and get the selection of statements.

Are you aware of such a tool?

  • 1
    Not sure whether this really helps you (thus comment): I use Jabref for my literature database. I can put key words for each paper, assign the paper to one or multiple groups, and I can put important statements into a "review" field. Commented Jul 30, 2014 at 8:02
  • Thanks for the hint but I am specifically looking for a way to not tag papers but only certain sections.
    – user20156
    Commented Jul 30, 2014 at 8:48
  • 3
    This gets very close to what social scientists call qualitative data analysis (as apposed to quantitative data analysis). There is software out there that does this. I have heard of ATLAS.ti, but I have never used it, as I am a quant not a qual. Another concern may be that such software could be overkill for your problem. Commented Jul 30, 2014 at 12:23
  • @MaartenBuis Yes that does look quite full-on and is probably not the simple tool I am looking for, thanks anyway!
    – user20156
    Commented Jul 30, 2014 at 12:49
  • how about using Evernote for this? you can create notes, which might even consist of a title only (e.g., your "Species A grew taller than Species B"). Notes can both be tagged and put into containers (notebooks). The search features is powerful, as it is full-text and can be refined using those tags. The note bodies might contain the full reference of the paper. Another way would be to put the reference as the title of the note, and any possible summary as the note body. The software is freemium, and for this use it would always be free to you.
    – user7112
    Commented Jul 30, 2014 at 13:04

3 Answers 3


I use Qiqqa to manage my PDFs when writing research papers. It allows you to highlight text or add notes to the PDFs. You can then tag the notes, and run "reports" which essentially will pull all of the tagged sections from all of the PDFs in your library into a single paper (similar to the Word document you mentioned) so you don't have to do that manually. It will show the original snippet from the paper, any notes you've made regarding that snippet, and the citation for the paper. There's also a neat brainstorm function that will let you visualize papers, tags, or notes and move them around/link them together; I use that to organize papers sometimes.

There is a free version which will let you try out some features, and an affordable pay version that has more enhanced options. There are some helpful how to videos on Youtube that provide a nice sense of functionality and may help you decide if it's the tool you're looking for. I've been using it since I started grad school and it's been tremendously helpful in organizing my academic writing.



I prepare a tex file for note taking (I learnt this by reading this answer to the question How to read and take notes on research papers) and I think that this method will help you. If you don't know how to work with LaTeX, it is very easy to learn; but you can make such file by means of any other typesetting software.

You can organize your notes by having each chapter or section for any of the papers you read. For instance, section 1 is for the first paper you read. Then you can use the makeidx package to tag the content and prepare an index for your notes. And after all, you can add references to your notes. Every sentence you write from a reference, you can cite it by putting a simple citation code in front of it.

So, by using three easy codes for indexing, referencing and preparing tables of contents; you will have a PDF file which is searchable, you have the references available and a table of contents which helps you to find your notes of papers. Also, you can categorize your notes of your papers by chaptering your file. For instance:

Table of Contents

  Chapter 1: Topic 1
     Section 1: Paper 1
     Section 2: Paper 2

  Chapter 2: Topic 2
     Section 1: Paper 3
     Section 2: Paper 4




  • You can easily find your notes of your papers.
  • You can have a references list of all the papers you have read.
  • You have an index, so can find the keywords you are looking for easily.
  • You have the papers you read categorized in each chapter, so you can easily manage your literature review and form the text you are writing.
  • You can copy and paste the content of your tex file to your report or paper.
  • You can print your file, or share it with a colleague or advisor for review.

Endnote can do such a task but you have to play a little bit with the fields in a reference.

Each reference entry in endnote has some fields, e.g. author, title etc. The aforementioned ones are typical in all references' entry. But, there are some fields entitled "custom". These custom fields can have whatever title you want and can be used in order to make smart categories.

E.g., I have used 2 custom fields. One for sub-fields of my field of study and one with notes. Based on the sub-fields, I have set up smart categories which hold papers-references with specific sub-field tag. Also, I can perform a search and EndNote will search also in the Notes custom field.

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