They are direct “competitors”. I find Zotero more power-user-friendly. For instance, there is a powerful bibtex plugin for Zotero that can run a server on localhost, so I can fetch the up-to-date bibliography for any particular collection from a make build with curl. I don’t see this hapenning ever in Mendeley
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.
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.
But unlike mendeley, it doesn't send you email advertising for PhDs based on the papers you have been reading it (getting it totally wrong I might add)
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.
It is completely isolated, if for example you want to include references in word. However some functions like adding references quickly with DOIs will fail without an internet connection.
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.
Even though I also like Zotero better because of its open nature, I prefer Mendeley in practice mostly because it has a decent Android client where you can just sync all your PDFs and read them on a tablet or something. Seemed a bit more involved to do the same with Zotero (where it seemed there were only minimal Android clients quickly hacked together). Mendeley also has 2GB storage, so that's nice for personal use and paper/book syncing.
That said, if I had to collaborate in a larger group I'd surely choose Zotero instead of locking everybody into some proprietary ecosystem.
But for personal use I definitely don't feel that I'm enabling or supporting Elsevier somehow in using their freeware.
> I definitely don't feel that I'm enabling or
> supporting Elsevier somehow in using their freeware.
If instead of using Elsevier's freeware you were to file bug reports - not code just reports - on Zotero then you could be helping improve the software.
And when you suddenly _do_ need to collaborate you'll find that you are using the same tool you have gotten used to, instead of the dissonance of using a tool that is similar-but-not-quite what you know.
I've not got any experience with Zotero, but I do with Mendeley. Unfortunately, the apps you've linked above suffer the same issues as many OSS alternatives to commercial software. For a start, the reviews on the Mendeley client [0] are far better than any of the three alternatives you've provided. All three of them have the same complaints - Functionality/UI leave a lot to be desired. My experience of this fragmentation (KeePass) is you have N clients which offer slightly different features, but none of them offer the same features that the commercial offering offers, meaning people who rely on one or more of the specific features of the commercial offering will never switch.
I have found syncing the PDFs via Dropbox works fine. Zotero puts them in a Dropbox folder with a reasonable filename, and then the regular embedded Dropbox PDF reader does an OK job on my phone/tablet.
It'd be nice to have the database synced, though. Funny how "synchronization of replicas of information", for all its centrality to modern internet-based life, isn't something that our operating systems provide as a system service.
> Funny how "synchronization of replicas of information", for all its centrality to modern internet-based life, isn't something that our operating systems provide as a system service.
Just FYI on that front, macOS has iCloud, which does this. I put something on my Desktop, it appears on all my machines. I can access it from my phone, etc. etc. - it's basically a built-in Dropbox.
That's great for synchronising files. It's not really the kind of thing that would help with synchronisation of, say, contact databases, email folders, shared text documents, calendars, bibliographies, photo archives, etc etc. It'd be interesting to consider an OS-wide API for flexible data synchronisation and conflict resolution.
Mendeley was very popular (until its unfortunate acquisition) because of its excellent PDF full text search and the ability to automatically get metadata (i.e. a bibtex entry) from PDFs. Can Zotero do that?
Because the info often isn't in the pdf file itself (at least in a parseable way). Typically metadata readers figure out what the paper is and then goes to a bibliographic database to pull out the full title, author list, page info, etc.
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.
Wow, that is seriously draconian. In my opinion it should be illegal if it isn’t, intentionally obscuring data storage to prevent marketplace competition.
"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 [...]"
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
> 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... ;).
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.
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.
Actually you can couple it to any WebDAV compatible cloud system. You can connect it to your own Nextcloud instance and have the limitations be your hardware.
It allows you to upload PDF or website snapshots, and by default an account is granted 300 MB free storage. They also have paid upgrades:
2 GB: $20/yr
6 GB: $60/yr
Unlimited: $120/yr
I've had the paid 2 GB plan for a while, I've got about 800 MB stored with them, and I've been very happy with the service.
Between the Firefox connector, the automated PDF OCR metadata lookup, and the ability to pull in metadata from DOIs, Zotero makes indexing things insanely easy. It's like MusicBrainz for articles. I'm always surprised how many obscure PDFs it correctly recognizes and indexes for me.
Personally, I just sync metadata and use my institutional Google Cloud storage for PDFs. A little more convoluted (I think this wouldn't work without the ZotFile plugin) but it appears to work across my 2 devices.
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.
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.
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!).
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.
Same reason booking.com shuttered the Hindi version of their website, educated Indians speak English and are very comfortable using it. When politicians have Hindi speeches written in Latin alphabet instead of Devanagari it shows something of the grip English has on the South Asian subcontinent, not just India.
>> I wonder why this comment got downvoted any without explaination. HN is not same, as it used to be.
Because this is a freeware program that is community-driven and you're blaming the developers when in reality it is the community that is failing to provide translations; largely the Indian language community, I might add.
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.
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.
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.
Your information might be outdated -- In the latest version of Zotero, when you add a PDF to Zotero, it automatically retrieves the metadata via DOI lookup.
(I don't think it would work with papers too old to have DOIs but haven't checked lately.)
The metadata retrieval pairs with a DOI or ISBN [1]. Articles without such handles might not work, nor will articles which are not OCR'ed (obviously) but this can be easily fixed with OCR scanning software.
The metadata retrieval process is a very handy feature, especially paired with Zotero's web browser plugin.
Zotero also keeps a repository of all the citation styles, which are curated and administered by the Zotero team and stored in a Github repo [2].
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...
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.
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.
It's a bit of a pain, but you can store `~/.local/share/okular/docdata/` in version control or your favourite cloud storage provider, and then you'll get synchronised annotations.
When I say a bit of a pain, I mean it - I switched to Mendeley with great sadness because its mobile application means I can read and annotate papers on my tablet and have it synchronised perfectly with my desktop.
On a semi-related note: the Mendeley mobile application makes selecting text a joy on a touchscreen with a kind of magnifying glass. I really wish it was built into Android system wide.
You have to explicitly save the file after making the annotations. I've been doing this for years with Okular, indeed, Okular having out-of-file annotations is news to me :)
yeah so I just reinstalled Zotero and imported my Mendeley library.
It does that, and it can actually look up metadata from pdfs.
But: It can NOT update already existing entries from such a lookup. You have to delete the pdf and re-import. Why? No reason.
It's this sort of really bad usability decision that makes Zotero just not very good imo.
I'm not sure what feature exactly you're missing, but are you aware of the "Rename file from parent metadata" option you get when right clicking on a PDF in the list? Perhaps that does what you need.
If not, with Zotero you have a chance of getting a missing feature added. Not so with the closed-source Mendeley. Especially now they have started doing user-hostile lock-in stuff like gratuitously encrypting users' data, making it no longer accessible to the user (see downthread).
With Zotero, in principle you could hack together something using `bash` and `sqlite3` that batch-updated documents; you may not even need to look at the source code to the official app. It's ad-hoc munging like that that Mendeley has recently gone out of its way to prevent, stopping people from working effectively with their own data.
Zotero can look up metadata if you add a PDF to your library
Zotero can not update metadata for a PDF you already have in your library
Hence, adding an existing library means you have to do it manually for each pdf
This is bad design, because the functionality exists, but it's implemented in a way that makes everything complicated for no reason at all.
Why disable the "lookup metadata" button for a pdf which is already in a library?
WHYYYYY
It's not a usability decision — it's just one feature that hasn't yet been implemented [1]. Updating metadata is more complicated than creating a new item, because you have to deal with the existing metadata somehow. (Mendeley just overwrites the existing item, often with incorrect data, which we don't consider acceptable.)
I really love the "duplicate finder" and its ability to pick and choose metadata to keep. Perhaps just create a duplicate item and deal with merge conflicts later?
>> 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..
It automatically added 90-95% of PDFs I imported, most directly from Sci-Hub with no editing from me.
My experience of auto-import of metadata in Mendeley is that it gets about 80% of it right. Not good enough for publication: I still had to check over each record with a fine-toothed comb when I wanted to actually use an entry to cite something.
So far, Zotero's metadata lookup seems about the same quality.
In the interests of nit-picking, back in the day I made some contribution to zotero's back end docs, and I was a bit unhappy with the way the open source project is managed as a potential contributor. But it's still pretty neat stuff.
Having recently persuaded my research group leader not to spend >£500 on Endnote licenses, this comment tickled me. It may even be the case that Endnote is now a largely functional piece of software, but its history is too exquisite an exercise in Worse is Better for me to go near it again.
Endnote. Ugh. When I used it a decade ago it was the worst program I have ever used. Try to look up something and nothing happens. Is it thinking? Is it connecting to a server? Did it just not find any results? There's no way to tell because it doesn't tell you anything.
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.
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.
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!!
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.
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/
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.
I second this workflow - thanks to Zotero and Ulysses I felt I was able to keep track of research for my thesis and easily restructure as I went along. My editor on the other hand was not so happy when I thought it was a good idea to use MS Word's built-in citation tool.. he made me pull them all out and add them back in manually. A good lesson to chat with your editor first before trying to be efficient.
Zotero's cross-platform plugins meant I could use any device for reading and not worry that if I followed important links I'd never find them again.
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:
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.
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.
167 comments
[ 2.4 ms ] story [ 164 ms ] threadI'd rather just use JabRef http://www.jabref.org/
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.
Reading about Elsevier now and I understand the objection. Thanks.
https://www.theguardian.com/science/2017/jun/27/profitable-b...
That said, if I had to collaborate in a larger group I'd surely choose Zotero instead of locking everybody into some proprietary ecosystem. But for personal use I definitely don't feel that I'm enabling or supporting Elsevier somehow in using their freeware.
If instead of using Elsevier's freeware you were to file bug reports - not code just reports - on Zotero then you could be helping improve the software.
And when you suddenly _do_ need to collaborate you'll find that you are using the same tool you have gotten used to, instead of the dissonance of using a tool that is similar-but-not-quite what you know.
Go ahead and use Zotero, check out the two or three leading Android clients, and file bugs. You've got these clients currently: https://play.google.com/store/apps/details?id=com.gimranov.z... https://play.google.com/store/apps/details?id=computer.benja... https://play.google.com/store/apps/details?id=net.ezbio.zote...
[0] https://play.google.com/store/apps/details?id=com.mendeley&h...
It'd be nice to have the database synced, though. Funny how "synchronization of replicas of information", for all its centrality to modern internet-based life, isn't something that our operating systems provide as a system service.
Just FYI on that front, macOS has iCloud, which does this. I put something on my Desktop, it appears on all my machines. I can access it from my phone, etc. etc. - it's basically a built-in Dropbox.
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
[2] 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
"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 [...]"
Is there a way to make it work with SciHub? Asking for a friend... ;).
https://www.reddit.com/r/scihub/comments/7ilwzv/scihub_look_...
https://github.com/bwiernik/zotero-tools/blob/master/engines...
http://www.docear.org/
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... [1] https://gtpedrosa.github.io/blog/apresentando-o-docear/ [2] http://www.jabref.org/
Could you use this like a digital "commonplace book"?
In the options under the Sync tab, I select WebDAV as the File Syncing type and for the URL I put:
with the appropriate credentials.Works flawlessly.
2 GB: $20/yr 6 GB: $60/yr Unlimited: $120/yr
I've had the paid 2 GB plan for a while, I've got about 800 MB stored with them, and I've been very happy with the service.
Between the Firefox connector, the automated PDF OCR metadata lookup, and the ability to pull in metadata from DOIs, Zotero makes indexing things insanely easy. It's like MusicBrainz for articles. I'm always surprised how many obscure PDFs it correctly recognizes and indexes for me.
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.
Still operating.
Update: I wonder why this comment got downvoted any without explaination. HN is not same, as it used to be.
https://www.zotero.org/support/dev/localization
Because this is a freeware program that is community-driven and you're blaming the developers when in reality it is the community that is failing to provide translations; largely the Indian language community, I might add.
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.
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
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.
(I don't think it would work with papers too old to have DOIs but haven't checked lately.)
The metadata retrieval process is a very handy feature, especially paired with Zotero's web browser plugin.
Zotero also keeps a repository of all the citation styles, which are curated and administered by the Zotero team and stored in a Github repo [2].
[1] https://www.zotero.org/blog/zotero-5-0-36/
|2] https://github.com/citation-style-language/styles
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.
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...
When I say a bit of a pain, I mean it - I switched to Mendeley with great sadness because its mobile application means I can read and annotate papers on my tablet and have it synchronised perfectly with my desktop.
On a semi-related note: the Mendeley mobile application makes selecting text a joy on a touchscreen with a kind of magnifying glass. I really wish it was built into Android system wide.
What kind of annotations are that? I think GP refers to document annotations, which are stored in the PDF file itself.
If they are stored in the file itself, that's news to me. Last time I used it, Okular didn't modify the actual PDF and considered that a feature.
Thanks!
It does that, and it can actually look up metadata from pdfs. But: It can NOT update already existing entries from such a lookup. You have to delete the pdf and re-import. Why? No reason.
It's this sort of really bad usability decision that makes Zotero just not very good imo.
If not, with Zotero you have a chance of getting a missing feature added. Not so with the closed-source Mendeley. Especially now they have started doing user-hostile lock-in stuff like gratuitously encrypting users' data, making it no longer accessible to the user (see downthread).
With Zotero, in principle you could hack together something using `bash` and `sqlite3` that batch-updated documents; you may not even need to look at the source code to the official app. It's ad-hoc munging like that that Mendeley has recently gone out of its way to prevent, stopping people from working effectively with their own data.
Zotero can not update metadata for a PDF you already have in your library
Hence, adding an existing library means you have to do it manually for each pdf This is bad design, because the functionality exists, but it's implemented in a way that makes everything complicated for no reason at all.
Why disable the "lookup metadata" button for a pdf which is already in a library? WHYYYYY
Disclosure: Zotero developer
[1] https://github.com/zotero/zotero/issues/1515
It automatically added 90-95% of PDFs I imported, most directly from Sci-Hub with no editing from me.
So far, Zotero's metadata lookup seems about the same quality.
For LaTeX users I recommend the Better Bibtex plugin, making my life a lot easier!!
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/
[1] http://raphaelkabo.com/blog/posts/markdown-to-word
Zotero's cross-platform plugins meant I could use any device for reading and not worry that if I followed important links I'd never find them again.
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."
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.
I've heard of other alternatives being better but shrug Zotero works well for us.