
Ask HN: What system do you use for tracking and annotating academic papers? - chollida1
I&#x27;m a bit embarrassed to admit that even though 75% of my time is spent reading and implementing ideas from academic papers, I really don&#x27;t have a great system for:<p>- recording notes and ideas from papers<p>- recording where I got a paper from, ie was it referenced from another paper or found on a particular site?<p>-  even how to read a paper.<p>Right now I use google docs with sub folders for unread, read and implemented papers.  I tend to use Acrobat to highlight sections of a paper that I find important and Evernote for saving more important notes.<p>If anyone has a good system for how to read papers more efficiently,  how to store notes&#x2F;annotations for a given paper, or how to track a todo reading list I&#x27;d be very appreciative!
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aheilbut
Mendeley is not bad at all. I save papers to a Dropbox folder, organized
directories by general topic / relevance to project. Mendeley (on one
computer) watches that folder, and imports the papers and fills out the
bibliographic info, mostly automatically.

Mendeley lets you tag and organize things in virtual folders, as well as store
notes and annotations. The bibliographic info for subsets of papers (eg. with
a particular tag) can be exported to bibtex files when writing.

Mendeley is available on all platforms, and syncs across multiple computers.
The only catch is that the links to PDFs are only maintained on the 'master'
that watches the folder. (If you try to watch folders on multiple instances of
the same synced database, all hell breaks loose.)

Pubchase (www.pubchase.com) can also sync with your Mendeley library, and does
a surprisingly good job of recommending papers of interest.

~~~
jessriedel
What is the advantage of Mendeley over Zotero?

My understanding is that Zotero implements essentially all of Mendeley's
features, and is free and open-source. (Here's the comparison according to
Mendeley: [https://www.mendeley.com/compare-
mendeley/](https://www.mendeley.com/compare-mendeley/) ). I think most people
just haven't heard of it. It's supported and developed by a foundation, and if
you ever stop liking it you can take all your data and move it to Mendeley
very quickly. On the other hand, I don't think it's easy to leave Mendeley:
[https://feedback.mendeley.com/forums/4941-general/suggestion...](https://feedback.mendeley.com/forums/4941-general/suggestions/1186641-bulk-
export-pdf)

EDIT: Here's how Docear compares them:
[http://www.docear.org/2014/01/15/comprehensive-comparison-
of...](http://www.docear.org/2014/01/15/comprehensive-comparison-of-reference-
managers-mendeley-vs-zotero-vs-docear/) Zotero lacks Android/iOS apps (except
for Zandy on Android, which is poor).

~~~
aheilbut
I should probably give Zotero another try. At the time I started using
Mendeley, it was really the best at automatically importing metadata for pdfs.
And I don't think Zotero does the watch folder thing.

One thing I do like about Mendeley is that it's content to leave my pdfs alone
in the filesystem (and I can rely on Dropbox for syncing those), whereas
Zotero seems to want to import everything and manage the files itself.

~~~
jessriedel
You're right about Zotero wanting to manage the PDFs. With regard to a watch
folder, there's ZotFile which works very nicely (but of course something
that's fully integrated is always preferable).

[http://zotfile.com/](http://zotfile.com/)

------
RogerL
PDFs in structured folders. I.e

    
    
        papers
        papers\filtering
        papers\math
        papers\languages
        papers\filtering\IMM
        papers\filtering\MHT
        

You get the idea.

When I read I highlight using the yellow highlighter, and type notes in
Evernote. Evernote is searchable.

I make this 'cloud'y by using bittorrent sync to share across computers.

That's all free. The folder method of holding papers/book/topics is nonideal -
a paper can cover 2+ topics, for example. But it works, sort of, and I can
still search. I use Everything (from void tools) to search on title or author,
and then you can search inside pdfs with various tools.

Mendeley and such were nonstarters for me. Any service that makes me pay for
cloud storage has lost the war, IMO. I already have 1TB each from Dropbox and
google, more from Microsoft, why am I paying you for cloud storage?

I was having trouble with syncing with Mendeley, but reading the other
comments aheilbut worked out the issues, so maybe i'll give it another go. I
want to control the cloud, syncing, and file structure choices, not have a
program decide those for me.

I don't worry about reading lists - I need to read what I need to read. When I
get around to that topic there may be more relevant stuff than I selected back
at the time, anyway. YMMV. If I see a paper of remote interest that I can
legally grab I grab it, dump it into my file structure, and then rely on
search to bring it to my attention again at the appropriate time.

------
bosie
I use Papers ([http://www.papersapp.com/](http://www.papersapp.com/)) and
DevonThink
([http://www.devontechnologies.com/products/devonthink/overvie...](http://www.devontechnologies.com/products/devonthink/overview.html)).

The latter holds my notes, highlights and every piece of information I find
somewhere; it can do basically any format, not just PDFs. Additionally it
links them up with other things in your database
([https://static1.squarespace.com/static/544bf5dae4b0dd27d7018...](https://static1.squarespace.com/static/544bf5dae4b0dd27d7018fa8/t/55acedcfe4b0b14a3f0ff0ba/1437396435522/)).
This plus the superior search makes retrieval a lot easier than in any other
application I have found so far.

~~~
quantisan
I use Papers too. I've set it up so that all my loaded papers are
automatically re-saved in a structured library as plain PDFs /Category/Year-
Author-Title.pdf. That library folder is on my Dropbox. So I can access it
anywhere else without Papers installed.

------
jessriedel
I use Zotero, with annotations typed as PDF comments. The biggest thing I am
lacking is a hardware device and compatible software for hand-written
notations that actually works smoothly in practice.

~~~
pedrodelfino
Same here. Handwriting is much better in order to retain the information,
science has already proved this. However, currently, there is not a very good
product (software and hardware) in the market to allow this. Unfortunately, I
still read important things in the printed versions.

------
88e282102ae2e5b
I disliked Mendeley, Zotero and Referencer. I've been thinking about going
back to just taking notes in a git repo in markdown (and keeping it on Gitlab
or somewhere else that renders markdown properly. Also uploading the PDF to
the repo alongside the notes, and having the main README have titles, DOIs and
links to the relevant notes. Obviously you can't make citations easy like in
any of the actual applications designed for this but I'm more focused on just
understanding the material for now.

------
wgjordan
For organizing your papers, Paperpile
([http://paperpile.com](http://paperpile.com)) is an excellent up-and-coming
reference management tool. It integrates with Google Drive and has a full-
featured PDF annotator and note-taker. It's helped me out tremendously in
organizing my academic research.

~~~
saboot
Paperpile looks especially interesting, especially since I already use google
drive to organize all of my documents. But $36 recurring yearly? .. Eh..

It would be nice if the single user mode was free, and the paid model included
the collaborative features.

------
therobot24
I use Qippa ([http://www.qiqqa.com/](http://www.qiqqa.com/)) simply because
it's fast. It's probably similar to Mendeley - i can tag, organize, mind-map,
highlight, share, etc.

------
jmathai
Surprised to see no one has mentioned Hypothes.is. Open source and already
being used to annotate academic/scholarly works.

[https://hypothes.is/blog/](https://hypothes.is/blog/)

~~~
dwhly
Thanks @jmathai.

I'm the founder of Hypothes.is, and here to say that we're delighted for
researchers us to use us in this way. So far, our primary emphasis has been on
collaborative annotation with others on documents vs individual annotation.
That said, we hope to layer on additional features where appropriate, and to
collaborate with other products and services when we can--particularly ones
that support open standards and open source software.

On Dec 1, we announced an initiative to bring an open annotation client to all
scholarly works over the next several years. [https://hypothes.is/annotating-
all-knowledge/](https://hypothes.is/annotating-all-knowledge/)

------
veddox
I use Mendeley, and have found to be quite good for my needs.

Previously I used ReadCube, which was also quite good - unfortunately it
doesn't run on Linux, so I had to ditch it. I would love to try out Citavi, it
sounds even better than Mendeley, but again it doesn't do Linux. (Note: Citavi
carries a fairly hefty price tag, but if you're affiliated with some
university, chances are you can get it for free. The other two are freeware
with the option to upgrade to premium plans.)

All of these are closed-source, so if you're an FSF-fan, steer well clear.
Otherwise: well worth the use of!

------
fsmunoz
Docear ([http://www.docear.org/](http://www.docear.org/)) + Zotero
([https://www.zotero.org/](https://www.zotero.org/)), with Emacs+AucTeX for
the writing.

They all fit together.

>\- recording notes and ideas from papers

Docear's core is a mind-mapping application that is used for taking and
linking to different notes - you can take notes using whatever app you want
and then add it to the mind map-

> \- recording where I got a paper from, ie was it referenced from another
> paper or found on a particular site?

With Zotero this can be as simple as a click, it adds the current page and
document along with metadata and can export it to bibtex or the like, thus
tying it to docear.

> \- even how to read a paper.

This is not a technology problem, investigate approaches such as SQ3R
([https://en.wikipedia.org/wiki/SQ3R](https://en.wikipedia.org/wiki/SQ3R))
which is the one I use (actually the variation SQW3R) or PQRST
([https://en.wikipedia.org/wiki/Study_skills#Reading_and_liste...](https://en.wikipedia.org/wiki/Study_skills#Reading_and_listening)).
I keep a low-tech approach on purpose for this, but there is nothing
preventing using Docear for this as well of course.

>Right now I use google docs with sub folders for unread, read and implemented
papers. I tend to use Acrobat to highlight sections of a paper that I find
important and Evernote for saving more important notes.

Docear is supposed to be used with PDF annotators, it then scans the PDFs and
automatically creates the references mind map.

> If anyone has a good system for how to read papers more efficiently, how to
> store notes/annotations for a given paper, or how to track a todo reading
> list I'd be very appreciative!

For reading them take a look at those I mentioned before, SQ3R has been useful
for me in terms of articles and books. To store things Zotero is very good for
anything which is done via browser. Docear is useful for managing different
"projects" (could be disciplines, specific papers, etc). For TODOs you can
either also keep them in Docear (since it has a mind mapper you can create a
new node and add the references you exported from Zotero there, actually
Docear scans the library and automatically adds any PDF to a specific node) or
use something like Evernote.

------
GFK_of_xmaspast
I use Zotero ([https://www.zotero.org](https://www.zotero.org)), and am liking
it a lot. (It's also independent, as opposed to Mendeley which is owned by
Elsevier)

------
huac
when I have to take notes from pdf's, webpages, and other sources, I've found
Word to still be the most effective. i paste relevant sections in (with a
macro to keep only text), and highlight the most important stuff. i have
macros set up for condensing text, cutting whitespace, click-and-drag
underlining

the biggest advantage of this is how flexible and easily searchable it is if
i'm working with different content types.

------
rdc12
Currently I am just using an org-mode file, but this is more like a reading
log along with a bit of meta-data (author, keywords etc).

So far it has suited my needs quite well, but I don't really annotate them,
but I do add a one or two sentence overview, which is enough for me.

------
gone35
Academic here. If you don't mind closed-source, use OmniOutliner.

------
zhte415
Email yourself if you're afraid of remembering.

Works for pretty much every kind of idea.

Then, just remember.

------
pen2l
Reuters' Endnote.

(have any of you guys tried it? Curious to hear your thoughts)

