Zotero is one of those pieces of open source software that has really improved my life. I first discovered it as a teenager and it revolutionised writing papers and managing sources. Sadly I don’t find myself using it that much in my job.
I always got a kick out of introducing it to my friends in the humanities and blowing their minds. I have no idea how anyone writes papers without zotero or another similar tool.
Keep up the good work.
The web plugin actually falls back to 'web page with snapshot' if it can't detect a journal paper, which in many ways is better than trying to drag around big PDF binaries.
Thanks! I've used zotero only minimally, mostly to support users of my software who use zotero, rather than using it myself for my own purposes.
Is the "web plugin" something built into zotero, or an extra plugin to install? Calling it "plugin" makes it sound like something extra to install, but not finding it easily googling. Help me out?
I think OP talks about the Zotero Connector Browser Plugin. So its not a plugin for zotero but your browser (Firefox, Chrome, Safari and Edge are supported)
The plugin ads a button to the Browser where you can add the currently viewed page to your database.
It even tries to detect references to papers or other content and choose the matching entry type. Eg on Google Scholar you can choose which search result you want to add. It its a PDF the file gets saved to your zotero database.
That is exactly how I use it and it works great for that.
Among other things, I love that I can subscribe to RSS feeds and then save individual items I want to be able to reference later on.
Before that I tried several things, local bookmarks, bookmark services (actually just delicious), and an org file for references, but Zotero is the most seamless system for knowledge repository for my use case.
What really blows my mind is how many of my academically inclined friends manage (and cloud sync) a big library of pirated papers using a rival piece of software owned by a major rights holder of said pirated papers. I mean... there's a good chance nothing will come of it, but it just seems like tempting fate. Zotero isn't just good enough, it's so good that the choice is completely trivial IMO!
I've converted all my colleagues to Zotero, even though the University has contracted subscriptions to EndNote et al. Zotero is just better. I wish that the UC System would contract with Zotero for their mutual benefit.
I had to use a trial version of Endnote 9 because a collaborator was using it. It was slow. Adding paper by DOI would freeze the interface for ten or more seconds on a database of less than 100 papers. Meanwhile adding a paper by DOI to my Zotero DB (curently 2000+ papers) is a snap.
It really is the superior product/project. I switched to Zotero from Mendeley this year. The thing that was keeping me back before was the lack of internal PDF reader and annotator. I'm not sure when that came into Zotero, but now it is... /chefkiss
I assume you're talking about Papers? The main feature is that there's an iPad/Android app that syncs really cleanly.
With Zotero, syncing reliably across multiple devices was always hit or miss for me. Saving a few papers throughout my day, going home and reading/annotating them on my iPad, and then going back to work and pulling up a paper from the previous day with its annotations intact is the dream workflow for consuming academic lit that has always just worked with Papers but always required a lot of effort with Zotero. Maybe this is more of a "me" problem than a Zotero problem, but if I can't configure Zotero to sync reliably then many academics won't be able to.
There are some other neat features too. The built-in reader is good enough to not bother going with a third party. The handling of in-text references is better than any alternative (the actual reference is listed when hovering or clicking the reference number in text–a seemingly basic feature that lots of citation managers and PDF readers don't have that is essential for maintaining concentration). The handling of figures, metrics, and smart suggestion of related articles is also top-notch. I was sad to make the conversion from FOSS but haven't looked back yet. Hopefully this new Zotero release will make it possible to transition back–it looks like lots of killer features in Papers are offered by Zotero 6, which is great to see.
As for the rights-holding thing, most journals give their authors the right to distribute their work for free upon request, and there are some other loopholes for getting papers afaik, so I don't think it would be worth the time or effort to go after people with a few sci-hubbed papers in their Papers account. I am afraid that DRM will make this much harder though, especially for papers that have been downloaded on a university network for later offline reading.
Does Elsevier really own Papers, Endnode, and Mendeley?
EDIT: no, it looks like Elsevier just owns Mendeley, which is what I was getting at. Uploading a bunch of papers to a company that's in a position to turn around and say "Those are some nice papers you uploaded to our servers, unfortunately they are evidence that you have fallen victim to piracy, now fork over $15k or we will be forced to proceed with a $15M lawsuit" just seems a bit reckless. Shrug.
I prefer Zotero, even though I would never even think of pirating a paper. Perish the thought!
To be fair Endnote license was given out for free and we didn't have to pirate articles as the university paid for all of these academic journal subscriptions.
The notes functionality along with the new iOS beta is amazing. Makes marking up papers on an iPad very convenient. I would encourage every who uses Zotero to sign up for a paid storage plan to help support development.
Truly amazing! I wonder if the iOS app in development will have all these note-taking features and work on iPad. If so, Zotero completely blows all of the competition out of the water at a price you can't really beat.
Not just for scholarly reference management: Zotero is a great tool to keep track of the books you have if your personal library exceeds one or two Billies in volume. For books printed after 1970 the ISBN alone is enough to have it fetch the most relevant metadata for any book published anywhere from online catalogues. I find Zotero particularly useful when going to a book-fair; it is easy to export a list of titles and authors of books you own so you can easily reference it to see which books from a particular author or series you already have.
Well-designed, proven, and sturdy though. It's not made of MDF, it's particle board. Although a cheaper material, this is actually a good thing here, because the same bookcase made of MDF would be much heavier and the planks would sag.
Prices are certainly on the high side, but that phenomenon does not seem limited to Ikea.
I love zotero. Amazing software, indispensable. Want an easy way to integrate with pandoc and Zim-Wiki, I'm sure there's a way but I've not found it yet.
You can use the BetterBibtex plugin to export the references to a bib or json file which can be ingested by Pandoc. There's an option to have it re-export the file every time you make a change to the library.
Citations work pretty well. You can customize the output with different CSL files [1].
I haven’t used their new iOS app, but it’s a welcome addition. In the past you had to sync your Zotero library with another app for PDF annotation that was synced (papership). It was never something I’d call robust or seamless and the papership app has felt like abandonware.
I’m still using qiqqa for my open source pdf search engine but the qiqqa team has moved on. Qiqqa has been a secret weapon for me in pulling up relevant paragraphs from research papers, ebooks, and standards that I have previously saved but not fully read.
Is anyone else getting horrible stuttering when scrolling that page? (I happen to be on mobile with a bad connection right now, but it's so bad it makes the page almost unreadable)
I used Zotero quite a bit in the past, the thing that ultimately drove me away is that when synchronizing you couldn't easily access the PDFs just via the filesystem. I use a nextcloud and also wanted to access PDFs from devices without Zotero installed and this turned out to be a pain at the time. Is this possible with more recent Zotero versions? Is the sync still cumbersome with a zotero account + self-hosted webdav?
I have a similar setup (Zotero + dropbox). Zotero syncs the entries and any notes, but dropbox takes care of the pdf storage. You can swap out dropbox for your storage of choice.
Files are all stored in a single folder (which can be in different locations depending on computer) which I point zotfile to. Inside that each paper is put into a folder based on author names. And each pdf is then renamed based on authors, year, and title.
I'm glad it includes some, but perhaps not the feature of storing pdfs in a different place so they can be easily synced via Dropbox? While I'd like to have as few extensions as possible, maybe I'll neat to keep Zotfile around regardless.
Zotfile is an extension that automatically converts internally stored pdfs to links in a filesystem directory -- the latter can be synchronized and accessed however you please.
It's been working great for me, although recent versions have a problem that it no longer recognizes the root directory and pollutes the zotero database with machine-specific absolute paths ((
I'm with Zotero for about 2 weeks and I'm very much in love with it. I use it mainly to store and categorize downloaded Websites (SingelFile) and PDFs.
While a PDF viewer (and every functionality that comes with it) is greatly appreciated, I'd wish for same for html and other formats. That'd be overkill :)
One thing that I really miss and actual slows my process, is a proper tag-system. Something like Anki has: being able to make tag hierarchies by higher-tag::lower-tag. I'm a heavy tag-user and the overall experience with tags in Zotero is very average. But maybe I'm using this application for stuff that's not intended for.
Overall great project and surely something I'll donate a few bucks to the next time I'm on that spree. You guys doing gods work. Love it!
I suggest to store them on de-duplicated filesystem or manually run fdupes and co to hardlink any duplicate in your Zotero lib because most modern websites are full of big js and zotero copy them countless of time, if you have a non marginal set of mirrored pages you probably waste more than 60% of occupied storage just in duplicates...
I have to check my folders for that. Since I am using SingleFile for downloading websites, I get single HTML files (as the name of the program says) so there shouldn't be any JS included...
I cannot tell from the changelog for this or the previous version whether Zotero has expanded its metadata and formatting capabilities to better support legal citations, so I guess I will stick to the Jurism[0] fork for now. If anybody knows of a better way to make this work in Zotero directly, I'm all ears.
It'd be so fantastic if the Zotero team could consider integrating their changes. I know that many probably won't necessarily need its advanced futures, but I see no risk of confusion as it's easy to use and mostly hidden in the "case" category.
The only thing holding me back from using Zotero is that, afaik, you need to use a Zotero account to reliably sync metadata between devices (the Zotero Data Server isn't supported). I wish it was easier to self-host; there's no reason for me to interact with their servers.
It's always a disappointment to find otherwise great open source projects that have key components that deny privacy.
Zotero supports WebDAV and I was using it with box.com without any troubles for years. What lured me to switch to Zotero's sync and cloud storage in the end, though, is the group library function.
Hint: You can sync the library for free by making an account. You need the "Zotero Storage" only if you want to sync the files as well. However, you can simply sync the folder ~/Zotero/storage using SyncThing. You could also use WebDAV, but SyncThing is just so much easier (set up & forget). The IDs/Metadata is consistent among syncs. :)
Of course, that doesn't resolve the privacy concerns, but personally idc about that.
edit: It seems like you might be able to sync everything by just putting ~/Zotero/ into something like SyncThing, avoiding the Zotero servers. But you'd probably have to be careful only opening the app after syncing has been completed. I haven't tested this though.
This is completely missing the point of GP. You can't (unless something has changed) sync metadata without using their servers. webdav is for the data, not the metadata. If you don't personally care about privacy, fine, but that's irrelevant here.
Replicating the local Zotero folder across devices won't properly sync the metadata in the face of concurrent changes.
If I didn't care about privacy and freedom I would have just used a proprietary product to begin with. It's an incredibly disappointing situation to have dragged on like this for so many years.
"Just fork it" is dismissive and misses the point. The criticism remains valid even if the maintainers refuse to act on it for whatever reason. Even if I were to invest the time to fork the project, the criticism would _still_ remain valid as long as upstream didn't take steps to fix the problem.
I‘m on windows, and here it is still possible. Try checking your settings again, it is a bit hidden: goto settings/sync, then file-sync -> via WebDAV is available in a Dropdown menu.
Yes, I wish they supported the server instance. Still, I don't mind subscribing to their syncing because it is probably the project's main source of revenue; although I am not for certain about that.
How good is Zotero as a bookmark manager similar to Pinboard.in or Raindrop.io? Both have a paid feature that stores a permanent copy of a site, but these are stored only on their servers, and Pinboard's archive download feature never worked for me.
I've used Zotero for over a decade to save webpages. It works fine in my experience, though I'd prefer if Zotero saved all the assets in a single file.
Zotero uses SingleFile. (Side note, this is, as far as I know, a destructive process—you can't recover the original bits. It would be interesting if Zotero switched to SingleFileZ and there were a sidecar file embedded in the ZIP container that would let you reverse the transformations to get the originals back out—or just store them directly.)
Zotero's snapshots work well enough on most pages you'd care to throw at it in an academic context. Your mileage may vary if you're using it as a general bookmarks manager, owing to the amount of client-side scripting-driven chicanery on the Web today. Notable example that I've found that Zotero didn't handle well at one point: Medium (although the data was there―the saved copy just wouldn't render correctly in-browser when opened; this doesn't appear to be an issue anymore for new snapshots, at least for now).
For most stuff that I want to have a durable URL for but that I feel doesn't merit being in my Zotero library, I just use ordinary browser bookmarks and make sure that the Wayback Machine and/or archive.is has a copy.
I'm probably stuck using Adobe for now, just because for anything really important you can't rely on anything aside from the official Adobe PDF editor to not screw things up. Up. But I absolutely love your project, I can imagine this would work great for academics.
You can automate much of your research between machine learning and directly reading PDFs. Many older publications don't have searchable text at all, and searchable text is a lifesaver when you're doing research.
After messing with the desktop version for a few minutes the note editor is weird. It doesn't modify the original pdf or the copy of the pdf it makes, the only way to get the highlights is to export it as a pdf. I expected something similar to Okular where edits would happen to the original file and update on ctrl-s.
Looks good, from whatever I have seen and read. I am going to give this a try.
A question to those who have used Zotero:
Can I opt to store everything on the local device and have zero data transferred to the server? Is there any kind of control over what is stored locally and what is sent to the servers?
My recollection is that it is all local by default. If you don't specifically connect to their web service for syncing data, none of the data is stored outside your local device.
By default, you can use Zotero without logging in, which will cause it to keep everything locally. It's not obvious how you might go about partially syncing to the cloud, however.
In practice, though you shouldn't store the SQLite in a cloud sync service, setting up a symbolic link for the backing PDFs in e.g. Dropbox works quite well and gives you more control over your data syncing. Then, you only need to rely on their cloud for the paper titles and metadata.
If I still was doing firmware dev, I could imagine this being amazing for dealing with datasheets, especially when shuffling between multiple parts all with their own descriptions of intended functionality, errata, and so-on.
This looks really nice. Zotero has never stuck with me for some reason but I last used it a few years ago. I'll try again.
One problem with this type of service is that there's usually a huge jump from unpaid to paid, but the jump to the lowest paid tier of Zotero lets you pay $20/year for 2 GB of storage. I can handle that. I have more difficulty with the $15/month and $90/year and such paid tiers. Even at $20/year, that comes to $100 after five years for what is largely a donation to support development.
One probably non-obvious thing is that the $100/yr ish unlimited storage tier includes everything you do as a user including shared libraries.
So if you have a group of people working together in a group library, one shared library subscription covers all of them. It doesn't take many people to make this worthwhile.
And as you say, it's a good way to support a great project. I do it even when I'm not really using the software.
> I do it even when I'm not really using the software.
I'll drop a one-time donation of $10 or $18 or something largely independent of my use - or even if I don't use it at all. I don't treat it as a purchase, though I can understand that others do.
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[ 9.2 ms ] story [ 524 ms ] threadI always got a kick out of introducing it to my friends in the humanities and blowing their minds. I have no idea how anyone writes papers without zotero or another similar tool. Keep up the good work.
Is the "web plugin" something built into zotero, or an extra plugin to install? Calling it "plugin" makes it sound like something extra to install, but not finding it easily googling. Help me out?
All in all very handy.
Among other things, I love that I can subscribe to RSS feeds and then save individual items I want to be able to reference later on.
Before that I tried several things, local bookmarks, bookmark services (actually just delicious), and an org file for references, but Zotero is the most seamless system for knowledge repository for my use case.
I doubt it can (otherwise everybody would be using it as a personal knowledge management solution, I assume). I'll take a look anyways.
What really blows my mind is how many of my academically inclined friends manage (and cloud sync) a big library of pirated papers using a rival piece of software owned by a major rights holder of said pirated papers. I mean... there's a good chance nothing will come of it, but it just seems like tempting fate. Zotero isn't just good enough, it's so good that the choice is completely trivial IMO!
Thanks, Zotero :)
[0] https://github.com/ethanwillis/zotero-scihub
With Zotero, syncing reliably across multiple devices was always hit or miss for me. Saving a few papers throughout my day, going home and reading/annotating them on my iPad, and then going back to work and pulling up a paper from the previous day with its annotations intact is the dream workflow for consuming academic lit that has always just worked with Papers but always required a lot of effort with Zotero. Maybe this is more of a "me" problem than a Zotero problem, but if I can't configure Zotero to sync reliably then many academics won't be able to.
There are some other neat features too. The built-in reader is good enough to not bother going with a third party. The handling of in-text references is better than any alternative (the actual reference is listed when hovering or clicking the reference number in text–a seemingly basic feature that lots of citation managers and PDF readers don't have that is essential for maintaining concentration). The handling of figures, metrics, and smart suggestion of related articles is also top-notch. I was sad to make the conversion from FOSS but haven't looked back yet. Hopefully this new Zotero release will make it possible to transition back–it looks like lots of killer features in Papers are offered by Zotero 6, which is great to see.
As for the rights-holding thing, most journals give their authors the right to distribute their work for free upon request, and there are some other loopholes for getting papers afaik, so I don't think it would be worth the time or effort to go after people with a few sci-hubbed papers in their Papers account. I am afraid that DRM will make this much harder though, especially for papers that have been downloaded on a university network for later offline reading.
EDIT: no, it looks like Elsevier just owns Mendeley, which is what I was getting at. Uploading a bunch of papers to a company that's in a position to turn around and say "Those are some nice papers you uploaded to our servers, unfortunately they are evidence that you have fallen victim to piracy, now fork over $15k or we will be forced to proceed with a $15M lawsuit" just seems a bit reckless. Shrug.
I prefer Zotero, even though I would never even think of pirating a paper. Perish the thought!
Happy to see the Markdown note linking, Safari extension, and native iOS apps.
[0] https://apps.apple.com/us/app/zotero/id1513554812
Possibly the most universal of all units of measurements. For the uninitiated: https://www.ikea.com/us/en/p/billy-bookcase-white-00263850/
Prices are certainly on the high side, but that phenomenon does not seem limited to Ikea.
Either way this software is massively underrated.
EDIT
What's with the official iOS app and no Android?
iOS is probably their most important platform. If there are enough users, I'd guess Android and Mobian apps will be forthcoming.
Citations work pretty well. You can customize the output with different CSL files [1].
[1] https://citationstyles.org/
I’m looking forward to trying the new app today.
Regardless, here is the direct link: https://apps.apple.com/us/app/zotero/id1513554812
I've tried EndNote. It's awful. Zotero is awesome!
https://jcuenod.github.io/bibletech/2021/07/26/full-text-sea...
I use zotfile (http://zotfile.com) to handle this.
Files are all stored in a single folder (which can be in different locations depending on computer) which I point zotfile to. Inside that each paper is put into a folder based on author names. And each pdf is then renamed based on authors, year, and title.
All of the above is customizable and automated.
But in some ways Zotero 6 makes filesystem workflows more complicated, in that PDF annotations don't get stored as actual annotations in the PDFs.
This is great to have consistent filenames from lots of different sources. Of course if the metadata is wrong or missing, it won't help.
It's been working great for me, although recent versions have a problem that it no longer recognizes the root directory and pollutes the zotero database with machine-specific absolute paths ((
While a PDF viewer (and every functionality that comes with it) is greatly appreciated, I'd wish for same for html and other formats. That'd be overkill :)
One thing that I really miss and actual slows my process, is a proper tag-system. Something like Anki has: being able to make tag hierarchies by higher-tag::lower-tag. I'm a heavy tag-user and the overall experience with tags in Zotero is very average. But maybe I'm using this application for stuff that's not intended for.
Overall great project and surely something I'll donate a few bucks to the next time I'm on that spree. You guys doing gods work. Love it!
[0]: https://juris-m.github.io/
I love the fact that open source software allows this but sometimes I really wish they'd just incorporate the two.
It's always a disappointment to find otherwise great open source projects that have key components that deny privacy.
Of course, that doesn't resolve the privacy concerns, but personally idc about that.
edit: It seems like you might be able to sync everything by just putting ~/Zotero/ into something like SyncThing, avoiding the Zotero servers. But you'd probably have to be careful only opening the app after syncing has been completed. I haven't tested this though.
Replicating the local Zotero folder across devices won't properly sync the metadata in the face of concurrent changes.
If I didn't care about privacy and freedom I would have just used a proprietary product to begin with. It's an incredibly disappointing situation to have dragged on like this for so many years.
Edit: Looks like nothing has changed. https://news.ycombinator.com/item?id=29774935
You are entirely free to use one of the many proprietary products...
Lol.
[1] https://www.zotero.org/support/dev/source_code
Zotero's snapshots work well enough on most pages you'd care to throw at it in an academic context. Your mileage may vary if you're using it as a general bookmarks manager, owing to the amount of client-side scripting-driven chicanery on the Web today. Notable example that I've found that Zotero didn't handle well at one point: Medium (although the data was there―the saved copy just wouldn't render correctly in-browser when opened; this doesn't appear to be an issue anymore for new snapshots, at least for now).
For most stuff that I want to have a durable URL for but that I feel doesn't merit being in my Zotero library, I just use ordinary browser bookmarks and make sure that the Wayback Machine and/or archive.is has a copy.
HN is also fond of Wallabag and ArchiveBox:
- https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
- https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
I literally pay 20$ a month to fill out PDFs
https://ocrmypdf.readthedocs.io/en/latest/index.html
I'm probably stuck using Adobe for now, just because for anything really important you can't rely on anything aside from the official Adobe PDF editor to not screw things up. Up. But I absolutely love your project, I can imagine this would work great for academics.
You can automate much of your research between machine learning and directly reading PDFs. Many older publications don't have searchable text at all, and searchable text is a lifesaver when you're doing research.
Unfortunately you can't just buy it,you need to subscribe to Creative Cloud
Other than that the editor is very well done!
A question to those who have used Zotero: Can I opt to store everything on the local device and have zero data transferred to the server? Is there any kind of control over what is stored locally and what is sent to the servers?
In practice, though you shouldn't store the SQLite in a cloud sync service, setting up a symbolic link for the backing PDFs in e.g. Dropbox works quite well and gives you more control over your data syncing. Then, you only need to rely on their cloud for the paper titles and metadata.
One problem with this type of service is that there's usually a huge jump from unpaid to paid, but the jump to the lowest paid tier of Zotero lets you pay $20/year for 2 GB of storage. I can handle that. I have more difficulty with the $15/month and $90/year and such paid tiers. Even at $20/year, that comes to $100 after five years for what is largely a donation to support development.
That's not that bad for a useful product, is it?
So if you have a group of people working together in a group library, one shared library subscription covers all of them. It doesn't take many people to make this worthwhile.
And as you say, it's a good way to support a great project. I do it even when I'm not really using the software.
I'll drop a one-time donation of $10 or $18 or something largely independent of my use - or even if I don't use it at all. I don't treat it as a purchase, though I can understand that others do.