
Zotero: An open-source tool to help collect, organize, cite, and share research - autocorr
https://www.zotero.org/
======
jknz
I use a little script [1] and a passive approach to quickly find a PDF I am
looking for among a few thousands of academic PDF. The workflow (illustrated
in the GIF [2]):

\- as I read new PDFs in the browser, the PDFs are passively downloaded
typically in a Downloads/ folder.

\- This results in thousands in papers lying in Downloads/ or elsewhere.

\- The command p from the script [1] let me instantaneously fuzzy-search over
the first page of each pdf (The first page of each pdf is extracted using
pdftotext, but cached so it's fast). The first page of academic PDFs usually
contains title, abstract, author names, institutions, keywords of the paper;
so typing any combination of those will quickly find the pdf.

What is particularly convenient is that no time is spent trying to organize
the papers into folders, or importing them into software such as zotero. The
papers are passively downloaded, and if I remember ever downloading a paper,
it's one fuzzy-search away. Of course it does not solve the problem of
generating clean bibtex files.

[1]: the script:
[https://github.com/bellecp/fast-p](https://github.com/bellecp/fast-p)

[2]: an illustration in GIF: [https://user-
images.githubusercontent.com/1019692/34446795-1...](https://user-
images.githubusercontent.com/1019692/34446795-12229072-ecac-11e7-856a-ec0df0de60ae.gif)

edit: The script has been moved from the gist to the public repository
[https://github.com/bellecp/fast-p](https://github.com/bellecp/fast-p)

~~~
sixdimensional
I love the passive nature of your workflow. I’ve always thought that, as soon
as I had consumed (read, viewed, heard) some content (text, audio, video) it
would be nice to have a “shadow copy” of it stored in a personal, private
knowledgebase, with a simple keyword or more complex semantic search on top.

Basically, a personal search engine with a passively gathered corpus of my
experienced content - maybe even filtered at times as in your case where you
limited it to academic PDFs (to keep the knowledgebase focused). Kind of like
an extension of our human memory.

Consume -> add as extension of knowledgebase -> recall.

Thank you for sharing your workflow - simple and ingenious!

Have you had any issues or thoughts for future enhancements? I can think of a
number of other helpful things you could do with the corpus you’ve built, for
yourself.

~~~
jknz
It is not limited to academic PDFs, although I mostly use the script to find
those. When typing academic keywords (author names, scientific jargon, etc),
the personal PDF that also lie in ~/Downloads/ are filtered out.

I recently used the command with some combination of airport/city/airline and
the only match was the boarding pass I was looking for. It could probably be
used for receipts from hotel or whatnot, as soon as pdftotext can retrieve the
text. It should find tax returns and related PDFs by querying "IRS + SSN".

A current issue that I would like to fix is the preview window that does not
always highlight the query in full if a single match was found before the full
query was typed. It is linked to how fzf handles previewing. I do not have
plans for any big enhancements.

edit: I created a public repo to replace the gist. Feel free to post your
thoughts or suggestions in the issues!

------
nanna
I used Zotero through my MA and into my PhD, when I discovered and began
writing in LaTeX in emacs/AucTeX instead of LibreOffice. I used the Better
BibTeX plugin [0] to maintain a BibLaTeX file, but as I developed my emacs
skills I moved to RefTeX.

At that point I realised that my BibLaTeX file was really a mess. Better
BibTeX created tons of needless double curly brackets {{like this}} in the
BibLaTeX file, making searching it directly a pain. And it created lots of
@misc entries, the BibLaTeX entry of last resort, when it should have made
@url's and other things.

Zotero has massively benefited my work, but it's also been something of a
training wheel which in the longer term slowed me down. Emacs/AucTeX/RefTeX
does everything Zotero does (at least according to my use) but faster,
cleaner, more holistically, and with more features (eg crossref'ing entries).
And two years on I'm still cleaning up that Better BibTeX's BibLaTeX file.

[0] [https://retorque.re/zotero-better-bibtex/](https://retorque.re/zotero-
better-bibtex/)

* edited because I confused AucTeX with RefTeX.

~~~
jhbadger
I guess I don't see how you can easily add citations without something like
Zotero (or its closed source equivalent Endnote). At least in my use case, I
go to Pubmed and click the Zotero Chrome plugin to add the reference to
Zotero. What do you do, manually enter the info?

~~~
nanna
Nah, not manual at all.

I just call up RefTeX by hitting ctrl-x + (or "C-x +" in emacs parlance). This
calls up a list of all possible references and a fuzzy search box which lets
me narrow it down. When I've found my reference I have ten options, including:

f1: Open associated pdf, url or doi

f3: Insert the citation into my thesis and then be asked for what kind of note
I want to add (footnote? Title? author name? Year? Just a bibliography
entry?), then any text to add before the reference (eg, "This argument has
been made by,"), then after (p. 67). -- This answeres your question

f7: Attach pdf to email

f9: Show notes, if there's an .org file of the same name.

f10: Add pdf to library

If RefTeX can't find my query, not only does it ask if I want to add a new
one, it asks whether to search various databases for it including arXiv, DBLP
(computer science bibliography), Google Scholar, Bodleian Library, HAL,
Library of Congress, British Library and others.

Adding entries to the database is as simple as editing a plain text file, and
BibTeX provides quick shortcuts for all the different kinds of entries, checks
them for you and provides a sane and customizable key.

Everything is completely integrated - my writing, my pdf library, my org
notes, my bibliography database, my email as well as my thesaurus (wordnut),
my pdf reader (pdf-tools) and my git repo (magit). It's just brilliant. All
together it makes emacs the ultimate writers tool, as far as I'm concerned.

~~~
cpbotha
I think what your OP was referring to is not adding a citation to a document
that you're editing, but rather ingesting PDFs and bibliographic data from the
web.

I love Emacs (not as much as you do it seems ;) but Zotero is amazing for
ingesting academic references including fulltext and bibliographic data from
the web. One click of a button in your browser, and everything is ready to
read and cite.

(Source: Wrote quite a number of papers and co-authored one textbook, all
using Zotero. My workflow was Zotero for ingestion -> per-publication bibtex
files for authoring)

~~~
nanna
Aha, apologies, my misunderstanding. Looks like I got a bit emaxcited 8)

So either you add them manually or you query Crossref, arXiv, DBLP or HAL
(French open archive) within emacs and then can copy their bibtex entry from
there. No pdf or web reference importer as far as I'm aware. Yet!

------
zwaps
I use Mendeley instead of Zotero. I really wanted to like Zotero, since I hate
Elseveir like the next guy, but Zotero didn't have any of the look-up features
and ability to quickly import my papers (thousands). In Mendeley, I can just
throw a physical folder into a folder and it'll tag and categorize the PDFs
mostly correctly.

I mean it is nice that Zotero has an import browser plugin (which, btw,
Mendeley does as well), but once you have a substantial library of pdfs, it is
just too time consuming to re-import it all again, type in names, years,
journals etc. ugh..

Also, Mendeley can open pdfs within the app and has great features for mark-up
and comments. Reviewing a paper is really nice this way. In fact, Mendeley is
the program with the best mark-up features on all of Linux, in my opinon. And
all this is synced across devices.

I'd love to use Zotero but tbh Mendeley is just better.

~~~
harry8
Mendeley is an Elsevier product? Might make a few academics come to a
differing conclusion given Elsevier's reputation is one they've well and truly
earned...

~~~
zwaps
I reinstalled Zotero just now, since it has a Mendeley importer now.

What is the proper way to store PDFs that I annotate (say, using Okular in
Linux) on Zotero with the ability to send them to other researchers and then
update them?

I don't mind paying money for cloud storage, but I gotta be able to work with
the pdfs.

~~~
ekphrasis
You can choose to set a custom PDF reader in the General tab of preferences
--> Open PDF using --> custom [1].

Then you can annotate the file and save it. If Zotero creates a copy of the
file when you save your annotations, you might need to use Show file by right
clicking the article in Zotero and make changes to the file in Zotero's
storage. In Linux, that'll be in ~/Zotero.

[1] [https://forums.zotero.org/discussion/1977/changing-the-
defau...](https://forums.zotero.org/discussion/1977/changing-the-default-pdf-
reader)

~~~
dstillman
No need to use Show File. You can just open the PDF from Zotero, annotate, and
save.

------
mblode
For my university essays, I keep my research citations in Zotero and write in
Markdown using Ulysses. Then when it is ready to submit, I'll use Raphael
Kabo's technique [1] to export into Microsoft Word. It is a truly simple
workflow to get perfect formating with little effort.

[1] [http://raphaelkabo.com/blog/posts/markdown-to-
word](http://raphaelkabo.com/blog/posts/markdown-to-word)

~~~
austinjp
Genuine question: what do you do with Word docs sent back to you as email
attachments with track changes and embedded comments?

I'm slowly realising that my colleagues for whom this "works" are never going
to change. Our shared folders are littered with "Copy of FINAL final +
comments 2.7.18-my-copy.docx.docx". It doesn't matter how slick my git +
markdown + pandoc workflow is when conversations go like this:

"Just use track changes."

"But..."

"JUST USE TRACK CHANGES."

~~~
alexchamberlain
Is your markdown to Word reversible? If so, accept all changes, convert back
to Markdown and run git diff. I guess you're losing comments though.

~~~
austinjp
Definitely worth a go.

Comments might be extractable, I'm not familiar with docx format but it's
zipped X(?)ML type data so there will be parsers. Or a conversion to an
intermediate format that's more amenable to computer processing, perhaps.

The problem remains in reverse, though: it's expected that I will produce Word
docs full of track changes edits.

------
michaelmior
I had tried Zotero before but I stuck with Mendeley for a long time. I ended
up using Zotero a couple years ago to share some references with my advisor
and since then I've grown to love it. One of the nice things about it being
based on Firefox is that there's a lot of extensions written for it (which
IMO, are not well-advertised).

The API is also great and I've been using it to automatically sync PDFs of
papers I want to read to my reMarkable tablet.

[https://michael.mior.ca/blog/zotero-remarkable-
sync/](https://michael.mior.ca/blog/zotero-remarkable-sync/)

~~~
geeio
Do you like the reMarkable tablet?

I currently have an iPad Pro but I really don’t like reading PDFs on it. I’d
love to stop printing out papers and an eink display would be nice.

EDIT: just read your review linked in the post

~~~
michaelmior
One thing I'll add that has happened since the post was made is that the
reMarkable team has been pretty good at churning out updates. The last
firmware update adds table of contents and text search for PDFs and its
incredibly fast.

My two biggest annoyances are currently:

1) No web app, so the only way to export PDFs is via the desktop app which is
only available for Windows and Mac. The Android app is also pretty terrible. I
think not starting with a web interface was a bad decision.

2) The PDFs exported from the desktop app are _huge_ (a PDF that started out
~400KB ended up >100MB after export). Support tells me they're working on
this.

------
wycx
5 years and 7464 references later Zotero has become an integral part of my
workflow. The combination of Zotero and the custom renaming of Zotfile lets me
store all my pdfs in Dropbox, but sync all database by Zotero such that I can
add references at work and have them waiting for me on my PC at home.

I abandoned Mendeley because it would not permit relative paths, and I have
not looked back.

~~~
131012
I loved zotfile for its feature which enable user to highlight/comment
articles then import the text in notes related to article.

~~~
degenerate
Our team switched from a custom solution to Mendeley last year instead of
Zotero because Mendeley lets you highlight and add notes in the PDF, which
gets shared among the whole team with those markups. Zotero didn't have that.
Otherwise we would have went with Zotero.

~~~
dstillman
In Zotero you just do that in your PDF reader of choice. If you're using
syncing, as long as the PDF reader saves annotations back to the original
file, Zotero will automatically sync the updated file to other group members.

The one downside of this approach is that multiple people can't modify the
same PDF at the same time. The upside is that you can use whatever PDF tools
you want and annotations remain accessible in the file even if you stop using
Zotero, which goes with our philosophy of leaving people in control of their
own data. (Mendeley stores annotations and highlights in its own encrypted
database, and you can't even export PDFs with annotations in batch. If you
want to get a PDF with your annotations out of Mendeley, you have to do it one
file at a time.)

Disclosure: Zotero developer

~~~
degenerate
Thanks for explaining how it can be achieved in Zotero. We did try this out,
but just as you mentioned, the annotated/highlighted PDF changes the file. We
liked how Mendeley keeps that information in a separate DB and lets you make
the markups right in the app, instead of having to do it yourself outside the
application. It was simply more seamless for our non-tech people.

------
montalbano
6 months to go before handing in my PhD thesis and I've just discovered it. It
was well worth the hassle of a slightly fiddly transfer from Endnote. Working
great so far.

For LaTeX users I recommend the Better Bibtex plugin, making my life a lot
easier!!

------
innocenat
Zotero really need more advertisement. I prefer Zotero over Mendeley, but
Mandaley seems to advertise much more to university.

~~~
tonyg
I have just recently switched away from Mendeley because of an insanely user-
hostile thing they've just done to lock-in their users.

Mendeley has started _encrypting_ users' bibliography files (from version 19),
claiming variously that encryption is required by GDPR (?!?!) and/or that it
improves security on a multiuser system. (Neither of these excuses holds
water.) The keys are not available to the users whose data were encrypted. The
encryption is completely proprietary and there are no tools available for
letting users work with the now-encrypted databases.

Previously, users could access their data by running `sqlite3` on a plain
sqlite database in their profile directory.

Not only did users take advantage of this, but a small ecosystem of third-
party tools and scripts had sprung up to help people take control over
automating repetitive tasks in managing their bibliographies.

Well, now Mendeley has encrypted everything, that's the end of that. No more
tools and scripts. No more user control over one's own data and workflow.

There's now only the limited (for my purposes, useless) "export database"
facility in the client. It only exports a limited subset of the fields in the
database. Alternatively, I could register as a developer, get an API key, and
develop a full web-style app to get hold of my own data. ("Did you just tell
me to go fuck myself, Bob?")

The Zotero people suspect that Mendeley's move was retaliatory for Zotero's
implementation of import-from-Mendeley [1]. The Mendeley twitter account has
dismissed this - literally - as being "fake news" [2]. Super weird.

I reverse-engineered the encryption they'd put in, in order to export my own
data and migrate to Zotero. I wrote up the instructions for others to follow
[3], but it's really not easy, not portable, not reliable, and not something
users should ever have to do just to get access to their own data!

Anyway, at this point, I don't trust Mendeley as far as I can throw them, and
I thoroughly regret ever recommending to my friends that they use the tool.
After nine years of using Mendeley, though, I've switched to Zotero, and it's
at least as good, and in some ways better. Plus it's properly open.

[1]
[https://www.zotero.org/support/kb/mendeley_import](https://www.zotero.org/support/kb/mendeley_import)

[2]
[https://twitter.com/mendeley_com/status/1006919608471818240](https://twitter.com/mendeley_com/status/1006919608471818240)
and several others. Really, the official twitter responses from Mendeley to
people discussing this issue were bizarrely dismissive and mocking.

[3] [https://eighty-twenty.org/2018/06/13/mendeley-encrypted-
db](https://eighty-twenty.org/2018/06/13/mendeley-encrypted-db)

~~~
yjftsjthsd-h
That sounds _against_ GDPR: [https://gdpr-info.eu/art-20-gdpr/](https://gdpr-
info.eu/art-20-gdpr/)

"The data subject shall have the right to receive the personal data concerning
him or her, which he or she has provided to a controller, in a structured,
commonly used and machine-readable format and have the right to transmit those
data to another controller without hindrance from the controller to which the
personal data have been provided [...]"

------
brailsafe
Zotero blew my mind when I discovered it last year. Works almost flawlessly.

I subsequently tried contributing but got lost in the weeds of the somewhat
unwieldy codebase. In part because it's interface is based on XUL and I don't
know wtf is going on there. I think they're slowly migrating to either
electron or something else. If you know XUL and have some free time, please
consider contributing.

------
rusbus
Wow what a throw back...I remember using Zotero in middle school over a decade
ago. It was a great tool then, glad to see they're still going strong.

~~~
SOLAR_FIELDS
I thought the same thing - It looks like they've come a long way since I used
it eons ago.

------
limbicsystem
Zotero rocks! I encourage all my students to use it as well even though the
University has a license from Endnote. Power tip: reduce the number of
characters searched from the default 500000 to more like 10000 for large (>5k)
libraries otherwise I find it slows down quite a bit.

~~~
Freak_NL
It makes so much sense to stimulate students to use a free tool they can keep
using after they leave university or change schools, without resorting to
piracy or expensive subscriptions ($250!).

------
pmontra
The site is not very clear about if it's possible to self host the server
part, but hopefully the server is the PHP application at
[https://github.com/zotero/dataserver](https://github.com/zotero/dataserver)

~~~
brailsafe
Yes. You can self-host a WebDav server and easily point Zotero at it.

------
th0ma5
Can I use this completely isolated and offline, or does it require you to use
it online or is otherwise severely limited if you don't? And it is easy to get
it in this mode in a clear way? Their website doesn't make this clear if this
is possible.

~~~
tonyg
Yes, by default it is completely offline. You have to take extra steps to
connect it to any kind of online service, such as a Zotero web account, or
Dropbox for file syncing.

------
gmac
I've used Zotero for about 10 years. Its one-click citation saving is awesome.

But since I am a LaTeX/LyX person, I also wrote an extension that lets Mac
users automatically add newly saved citations to BibDesk:
[http://mackerron.com/zot2bib/](http://mackerron.com/zot2bib/)

------
nerdponx
Zotero really needs to become self-hostable. Other than that, it's a great
tool.

------
TeMPOraL
> _Zotero is the only software that automatically senses research on the web.
> Need an article from JSTOR or a preprint from arXiv.org? A news story from
> the New York Times or a book from a library? Zotero has you covered,
> everywhere._

Is there a way to make it work with SciHub? Asking for a friend... ;).

~~~
voxadam
A quick DDG search lead me to this:

[https://www.reddit.com/r/scihub/comments/7ilwzv/scihub_look_...](https://www.reddit.com/r/scihub/comments/7ilwzv/scihub_look_up_engine_for_zotero/)

~~~
krrrh
Can confirm, this works.

------
paultopia
I want to love Zotero, I really do. But the last time I tried it seriously, I
found that:

\- metadata extraction/automated adding really doesn't work right with my
research workflow (a lot of google scholar searches, a lot of humanities and
social science sources)---lots of inaccurate or incomplete info, lots of
downloading RIS files and then manually importing and separately manually
importing the PDF.

\- documentation for things that would be useful like hooking up to academic
library proxies is nonexistent. Take a look at the chain of empty links when
you try to get proxy info:
[https://www.zotero.org/support/proxies](https://www.zotero.org/support/proxies)

\- no better bibtex for zotero 5... Although maybe this has changed recently?
Which would be amazing.

~~~
dstillman
> metadata extraction/automated adding really doesn't work right with my
> research workflow

I'm not sure exactly what you mean, but the primary way of adding items to
Zotero is with the Zotero Connector browser extension, which lets you save
high-quality metadata and PDFs with a single click from a huge variety of
sources (certainly including humanities sources, since Zotero was created by
historians). No other tool comes close to Zotero's abilities here. Metadata
quality does vary by site, though — Google Scholar specifically only provides
limited metadata, so you'll often get better results by clicking through to
the linked article and saving from there. We have plans for functionality to
flesh out incomplete metadata retrieved from subpar sources.

Zotero can also automatically retrieve metadata from PDFs you drag in, which
should work for the vast majority of recent PDFs and many older ones with DOIs
assigned, though that's not meant to be the primary workflow.

> documentation for things that would be useful like hooking up to academic
> library proxies is nonexistent

Current proxy documentation is here [1], and that's what's linked from the
main documentation page. I've fixed the outdated page you pointed to — thanks.

Note, though, that the proxy functionality is meant to work automatically for
the popular academic proxies, so most people don't need to configure anything
to use it. (And as far as I know other competing tools don't offer anything
like this.)

> no better bibtex for zotero 5

BBT has worked with Zotero 5 since last year.

Disclosure: Zotero developer

[1]
[https://www.zotero.org/support/connector_preferences#proxies...](https://www.zotero.org/support/connector_preferences#proxies_preferences)

~~~
paultopia
Thank you---this is super encouraging, and a good signal to maybe go back to
it.

Incidentally, one thing that would be really helpful for a documentation
standpoint would be a series of articles about best practices, like which
metadata sources work best.

------
rotskoff
I recently switched to Zotero from Papers, which is only for OS X and I needed
to work on a Linux computer. After Papers was acquired by ReadCube, I was also
concerned it would end up like Mendeley, which has a social network model that
I don't particularly like.

On the whole, the transition was pretty effortless and I am pleased with
Zotero (plus the Better BibTex plugin and webdav syncing). I like having the
rss feeds inside the client. The firefox add-on is far superior to the Papers
version. And finally, because it's an open source project with a reasonable
ecosystem, many of the things I found annoying about Papers have been solved
(like customizing which fields to exclude from a bibtex export).

~~~
phren0logy
I have been really happy with ReadCube. It's kinda clunky and awkward in some
places, at least compared to Papers, but it works very well. I'm a happy
paying customer.

------
singingfish
Zotero is awesome. 80% of the academic type people I've introduced it to have
switched. The other 20% have Endnote stockholm syndrome.

~~~
jhbadger
Particularly bench biologists tend to have "The only way to write a paper is
Microsoft Word and Endnote". Zotero is considered a bit eccentric and using
LaTeX is practically unheard of. As a computational biologist I like Zotero
and LaTeX but am often forced not to use them in collaborations.

~~~
singingfish
I wrote my (social science) PhD with LaTex (eventually). Corralling it to
BibTeX from Zotero was a bit of a pain, but worked fairly smoothly. What it
did achieve was that it made it look like I had paid much more attention to
layout and cross referencing than I actually had, which got me through with
two nit-picking corrections.

------
techbio
Important supporting institutions. GUI looks like a lot of overlap with
Citavi.

[https://www.citavi.com/en](https://www.citavi.com/en)

Major differences seem to include cloud based Zotero's advantages for sharing,
collaborating, and Citavi's better fine-grained document quote/cite tools.

[https://www.quora.com/What-is-the-difference-between-
Citavi-...](https://www.quora.com/What-is-the-difference-between-Citavi-and-
Zotero#)

------
danielecook
I am a big fan of paperpile:

[https://paperpile.com](https://paperpile.com)

I've used Endnote, Mendeley, and Zotero before and found them all to have
their own issues. Paperpile is not perfect but it shines in a few places and I
really like it. The chrome plugin adds an 'add to paperpile' button to places
like google scholar making it easy to add citations.

It also is designed for writing in Google Docs and makes it very easy and
quick to add citations. For some, Google Docs may be a dealbreaker, but if you
need to collaboratively write/edit a manuscript it's much better than the
alternatives in my opinion (esp. because everyone can write/edit at the same
time).

~~~
innocenat
Zotero also have chrome plugin that, while I don't remember it work on Google
Scholar, I use it all the time on actual journal site (IEEE Xplore, arxiv,
Nature, ACM, etc.)

------
zip1234
I used Zotero while going through University and it seemed revolutionary at
the time. There wasn't really anything else that could properly import the
citation info from journals, web sites, etc so easily. Most of them you would
have to type everything in manually. Zotero changed all of that and truly made
it easy. Glad to see that it has kept getting better and better.

------
icelancer
My company's R&D department uses Zotero a lot for our academic publishing.
It's a little steep to get started as you build out the database but it's
incredibly handy and well worth the time investment.

I've heard of other alternatives being better but _shrug_ Zotero works well
for us.

------
dangom
I'd like to switch to Zotero, but I've been using Mendeley for a good 5 years,
and built a decent workflow around it. I was wondering if anyone here took the
leap and made the switch, and could perhaps point out some of the biggest
differences between both tools?

~~~
tonyg
I did, just recently; the biggest difference, to me, is that you have to
configure synchronisation of PDFs yourself, if you don't want to use the
Zotero web account thing to do it for you. I haven't tried the Zotero account
file-syncing option, myself; I just use the Zotfile extension to make it copy
the files to a Dropbox folder.

ETA: The firefox integration of Zotero is _great_ , and something I missed
from Mendeley. Also, I should say, before I switched to Zotero, I was a
Mendeley user for about nine years, and did my PhD dissertation's bibliography
using it. I'm quite confident Zotero would have been just as good.

------
SubiculumCode
I used to use Zotero exclusively for managing citations in my papers. In the
end though, I always had to correct many errors in the reference section. This
is not Zotero's fault; the journal sites and indexes from which Zotero gleaned
it's information are often incorrect or incomplete. Not to mention that many
journals do not follow a standard MLA/APA, etc, but a custom format, which
always required me to do more edits. Now days I just do it all by hand. Not
sure if things have since gotten better since 4 years or so ago since I last
used it.

That said, Zotero as a research tool for organizing papers by topic,etc,adding
notes, is just fantastic. I really do love Zotero and it's potential.

------
peebz
I've tried Zotero but have been using JabRef
([http://www.jabref.org/](http://www.jabref.org/)) for a good few years now
and it works well for me on Linux.

------
voxadam
Docear is another interesting project. Unfortunately though, Docear isn't
nearly as active as it once was.

[http://www.docear.org/](http://www.docear.org/)

~~~
gtpedrosa
I came in just to give a shout out to Docear as well. There is an extensive
blog post comparing Docear, Zotero and Mendeley made by Joeran Beel (Docear's
team)[0]. I can't recommend it enough. It helped to get the review of my MSc
thesis done easily combining a mind map approach to actually cliackable pdf
links (in sync in multiple pcs), all this with bibfile integration. I actually
blogged about it in portuguese [1].

However due to the literary suite paradigm I would recommend Jabref (which is
integrated in Docear) instead [2], if you are coming from Zotero/Mendeley,
which is what I Did. Docear alone is capable of much more. I was not aware it
is not really active these days. It is really unfortunate.

[0]
[https://www.scss.tcd.ie/joeran.beel/blog/2014/01/15/comprehe...](https://www.scss.tcd.ie/joeran.beel/blog/2014/01/15/comprehensive-
comparison-of-reference-managers-mendeley-vs-zotero-vs-docear/) [1]
[https://gtpedrosa.github.io/blog/apresentando-o-
docear/](https://gtpedrosa.github.io/blog/apresentando-o-docear/) [2]
[http://www.jabref.org/](http://www.jabref.org/)

------
Freak_NL
I use Zotero to maintain a catalogue of the books I own. Being able to find
the metadata for almost any book just by typing the ISBN (10 or 13) in the
search field is a really nice feature.

------
ib84
I'm a big fan of Zotero. One of the greatest features is that you can use your
own WebDav-Server to store and sync PDF files. There is also this tutorial on
how to install your own Zotero server [1], but I don't know how to config
Zotero to use it. Anyone knows?

[1]: [http://git.27o.de/dataserver/about/Installation-
Instructions...](http://git.27o.de/dataserver/about/Installation-Instructions-
for-Debian-Wheezy.md)

------
therealmarv
Used back in the day Zotero Bibtex export with Markdown and this
workflow/template
[https://github.com/tompollard/phd_thesis_markdown](https://github.com/tompollard/phd_thesis_markdown)
for my thesis. Zotero is very good (especially with extension on the browser,
it's like pinning something in Evernote) and the best is: it's free.

------
black_puppydog
Being able to quickly import literature via embedded metadata or specific
extractors within zotero is incredibly convenient.

They have a super simple interface to do this from firefox, but I also
configured my qutebrowser via a userscript:

[https://github.com/parchd-1/qutebrowser-
zotero](https://github.com/parchd-1/qutebrowser-zotero)

------
anfractuosity
I see references here about zotero being able to look up metadata for a pdf.

I'm slightly confused what that means, is that just meta data in the pdf file,
that isn't visually visible?

For a while I've wanted to make something that can extract the title, authors,
and bibliography visually from a pdf. Is that what zotero can do also?

~~~
dstillman
It doesn't use embedded metadata in the file, which is usually pretty low
quality. It looks for various identifiers (DOI, ISBN) in the first few pages
that can be used to retrieve high-quality metadata from external services. It
also does some analysis to try to identify the title, authors, abstract, etc.,
and compares those against known metadata for further lookups and/or to
supplement the retrieved metadata. (This is a web service [1] because of the
database requirements, but we don't log any data about the contents or results
of searches, and it's an optional feature.)

For extracting metadata from a formatted bibliography you can use AnyStyle
[2], which is a separate service written by a Zotero developer.

[1] [https://github.com/zotero/recognizer-
server](https://github.com/zotero/recognizer-server) [2]
[https://anystyle.io](https://anystyle.io)

~~~
anfractuosity
Gotcha, thanks a lot for your reply!

------
beezischillin
We also used Zotero during our university studies for keeping track of
citations. It's a great tool!

------
lxhrstn
I used to use Zotero and Mendeley, but recently switched to Paperpile and
haven't looked back. It's a Chrome plugin, and saves all your papers to Google
Drive. It has a really nice cite-while-you-write extension for Google Docs
that really makes it worth it.

------
tzm
Excellent to see and plan to try it out. I almost exclusively use DEVONThink
Pro for collecting, organizing and searching local documents and Web
resources. It's a key part of my research workflow, but always open to testing
(or creating) improved tooling.

------
staamen
Always been a very happy Zotero user throughout my degree to manage my
citations. Without it writing papers would have been a much bigger headache.

------
philgooch
Zotero is great, does everything except actually read your papers for you.
Although, there is a tool out there now that does that.

------
ib84
Assuming you managed to install your own Zotero sync server (not webdav), does
anyone know how to use it with the Zotero client?

------
puzzlingcaptcha
The ability to host your attachments (.pdf files mostly) on your own WebDAV
server is very useful.

------
aq3cn
This software is available in 30+ langauge, but not in any Indian langauge. I
wonder why developers Ignore translation of softwares in Indian Languages. If
dev team is reading this, please contact me. I would translate this software
in Hindi language.

Update: I wonder why this comment got downvoted any without explaination. HN
is not same, as it used to be.

~~~
Freak_NL
Translators are welcome to help. Read this:

[https://www.zotero.org/support/dev/localization](https://www.zotero.org/support/dev/localization)

~~~
aq3cn
Thanks, I will do the the translation in my free time. I hope other people
also join in.

------
jkh1
I don't want a third party cloud-based solution and Zotero is not clear on
where your data is by default. So I went with JabRef
([http://www.jabref.org/](http://www.jabref.org/))

~~~
detaro
it says literally on the Zotero front page that all cloud functions are
optional.

~~~
jkh1
Yes but it isn't clear to me whether it's enabled by default.

------
foobarbecue
Happy zotero user for the last decade here.

------
Sabinus
Feature request: integration with Sci-Hub

~~~
levesque
That's not gonna happen, unless they dislike being sponsored/funded.

------
est
reminds of an ancient site called diigo.

Still operating.

------
patrickg_zill
Does it only store the metadata or does it have the power to store the full
text, whether pdf or website or other document?

Could you use this like a digital "commonplace book"?

~~~
Schiphol
You can store pdfs and other article files, and sync them across devices. The
first 300MB are free, and there are 2GB, 6GB, and unlimited-storage paying
tiers.

~~~
brailsafe
You can also just set up a WebDAV server and sync that across devices. Works
pretty damn well.

~~~
Schiphol
Huh, that's interesting! Do you know of a blog post where this is spelled out?

~~~
phireal
I use my Nextcloud install (since it provides a WebDAV interface).

In the options under the Sync tab, I select WebDAV as the File Syncing type
and for the URL I put:

    
    
        my.nextcloud.server.com/remote.php/webdav
    

with the appropriate credentials.

Works flawlessly.

~~~
Schiphol
Thanks a lot :)

------
maym86
Looks like [https://www.mendeley.com](https://www.mendeley.com)

~~~
hyeonwho4
Mendeley is supported by Elsevier, closed-source, and has premium-only
features only for institutional users. Its publisher affiliation is important,
when you see things like "Mendeley supports responsible sharing."

Zotero is the full package, GPL, the only premium service is extra data for
syncing with their server (not necessary if you only have one client). None of
this Orwellian hinting about keeping researchers from using libgen.

~~~
maym86
Yeah. Was just sharing it because it's what I used 5 years ago for my PhD.
Worked well at the time and I found it useful. I don't think Elsevier owned it
then. Got heavily down voted so I'll take the hint :)

Reading about Elsevier now and I understand the objection. Thanks.

[https://www.theguardian.com/science/2017/jun/27/profitable-b...](https://www.theguardian.com/science/2017/jun/27/profitable-
business-scientific-publishing-bad-for-science)

------
msconnect
It is ok not great. Lack many features. If they make app they can bring in
many features from other citation managers very simple way. But all the
citation managers out there half cooked softwares and so is this one. It is
just a very basic tool with no features. Mendekey is better, papers is good,
endnote is good but all those are expensive and not free except mendeley. So
if they want it for just a regular bare minimum use tool then it is ok but
otherwise power users and more trouble free versions are as mentioned above
however these paid softwares also lack serious features even after paid. So
you can’t expect much from free versions. Also zotero design is not sleek
clean. It looks very raw and clumsy. Which can be easily improved by better
interface design.

~~~
ipstone2014
people should try readcube.com, it's not free, but the best I can find to
organize papers/references from any platform (iOS, android, pc/mac/linux).

