17 ms·

Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

• benjamir 5y ago
  We tried to migrate a reference library with more than 17k entries, but it never worked out beyond 2k. Sorry to say: might be fine for small personal projects, for anything serious I don't see how.
  • chana_masala 5y ago
    What were you trying to migrate from? And what do you use now?
  • wcerfgba 5y ago
    What problems did you encounter with this large library?
    • benjamir 5y ago
      The import via API failed too often.
  • dstillman 5y ago
    Something's not right there. People use Zotero with libraries with tens of thousands of items all the time. (Some people have hundreds of thousands of items, though that gets dicier.) Not sure exactly what you were seeing, but we'd be happy to debug in the Zotero Forums if you wanted to try again. It's possible to configure a third-party plugin such that it affects performance, for example. (Disclosure: Zotero dev)
  • zoomablemind 5y ago
    Isn't zotero backed by sqlite db? So these row counts are nothing much to cope with, sqlite would do just fine. Do you mean it did not work out for you performance-wise or the export process failed?
  • urschrei 5y ago
    I’ve been using Zotero since it was in beta in 2007, and have a library with tens of thousands of items. As dstillman says that’s hardly unusual. It works perfectly (it’s just a SQLite db with a mature, well-designed schema after all), and syncs perfectly across five devices.
    • benjamir 5y ago
      Funny, we tried probably your solution for imports? urschrei/pyzotero is yours? Failed all the time. To be fair we got a lot of 5xx, so maybe we were just out of luck. Anyway time ran out with that project.
      • urschrei 5y ago
        I can imagine many reasons why attempting to create 17k items via the web API without some kind of batch processing and/or rate limiting may not have been a successful endeavour.
• designium 5y ago
  I use Zotero as a bookmarking too. It saves the files and articles offline.
  • wcerfgba 5y ago
    Same!
  • Brakenshire 5y ago
    Do you know if you can do full text search for saved webpages? That would be useful.
    • dstillman 5y ago
      Yes, Zotero can do full-text search of PDFs, webpages, and text files. It can also sync the full-text index separately so that you can do full-text searches without keeping the files on every device. (Disclosure: Zotero dev)
  • solarkraft 5y ago
    Can you do highlighting in the browser as well? Then it might be absolutely amazing. I outlined what I'm looking for here: https://news.ycombinator.com/item?id=29776997 https://news.ycombinator.com/item?id=29776997 Do you think this might be possible with Zotero after all?
    • cxr 5y ago
      Use Hypothesis to highlight/annotate. Optionally import them into Zotero with the Hypothesis-to-Zotero tool, if that's where you want them.
• chana_masala 5y ago
  I found Zotero very confusing to use. But maybe I am not the target demographic. I have always just used vim txt files for notes, using cli tools like grep to find what I need.
  • mbreese 5y ago
    It is very good for also downloading and keeping track of PDFs. It is primarily targeted at academics. And for many of us, it’s a great tool for keeping track of what papers we are currently reading, or want to keep for later. It can be hard to manage citations, PDFs, etc… in a text document. I know some people do, but I like being able to use a bookmarklet/extension to add a new paper to my lists.
  • nvrspyx 5y ago
    To add to the other comment, Zotero can also download the PDF for you if you just have a citation (if it can find it) and it also integrates into Word, Google Docs, etc. for citations when writing research papers. It's especially useful for multiple people writing the same research paper as the library can be shared.
    • lfmunoz4 5y ago
  • prepend 5y ago
    Generating the citation text in whatever format people like is a time saver.
    • kergonath 5y ago
      More like a life saver. It is hard to imagine the time it takes to fix references in a review article, never mind a PhD thesis, even with a proper bibliography tool. A bit less so with LaTeX, but still very useful.
  • jccalhoun 5y ago
    It sounds like you might not be the target demo. Zotero is mainly for generating bibiliographies not note taking. It has notes in it but it is pretty basic.
• simlevesque 5y ago
  I learned it in college and a month ago I was googling to remember this software and I found nothing. So thank you for posting this !!
• wosk 5y ago
  I highly recommend going for the beta version which features a (game-changing) built-in pdf reader[1], with annotations (searchable and synced with the beta iPad app) and many more improvements. Zotero is an amazing tool and I could not imagine writing papers without it. For collaborative writing, it syncs the bibliography with overleaf[2] and google docs. The browser add-on allows to build your library with one click while browsing, and it parses wonderfully meta-data from all (most) publishers and pre-print servers. Then my unique bibfile (symlinked in every project) is continuously updated to reflect new items or manual changes. But I use it even for non-publishing side of research: one can save webpages (with snapshots) and write notes with formatting around them. My personal research workflow involves note-taking with the markdown app Zettlr[2], from which I can cite my Zotero library using simply `@[Author:Title:Year]`. I can then build notes from a twitter thread and stats.stackexchange.com answers, then connect it with papers and blog posts that way, and a specific chapter of a book with my annotation on the cloud. It not always straightforward as a workflow but it works wonders. And the team is very responsive on the forum and on twitter. If one of the dev is ready this, thank you so much for making researchers life way easier ! EDIT: I just realised I can share my libraries online. A bit ashamed because it is very messy, but in case you are wondering what a Zotero library looks like, here is the link to mine [4] (without the notes and the embedded pdf and data files because I cannot share all of them. Moreover, I don't use the folder structure anymore so its very messy). [1] https://www.zotero.org/support/pdf_reader_preview https://www.zotero.org/support/pdf_reader_preview [2] I recommend the BetterBibTex extension for anything related to tex, it'll save you a lot of time [3] https://zettlr.com https://zettlr.com, another great app. [4] https://www.zotero.org/wosk/library https://www.zotero.org/wosk/library
  • jjoonathan 5y ago
    Ooh, cool! I'm spoiled by liquidtext, and while this isn't at the same level yet, I'm glad they're headed down this path because liquidtext recently went Scrooge McDuck with the pricing.
  • bluenose69 5y ago
    Thanks for pointing out the built-in PDF reader. I use the beta version but was quite busy last term, and hadn't noticed this new feature. It's handy because it lets me highlight and take notes without affecting the PDF file.
• smitty1e 5y ago
  I use Zotero to manage the research with: - the FireFox connector for ingest, - export to bibtex, and - the "Zoo for Zotero" app from the Play Store to pull the content down to a Samsung tablet for portable reading.
• tehjoker 5y ago
  Zotero saved my life writing research papers. You can get all kinds of plugins to Sublime or Google Docs for adding citations.
• prepend 5y ago
  I use zotero for managing research and bibliographies. But it’s so weird that their web version (the only one I’ll ever use) doesn’t make it easy to share bibliographies with other people. It’s such a weird feature that’s missing and it really important when collaborating on a paper. It’s free and better than the alternatives I’ve tried (endnote, mendeley, Google docs)
  • wcerfgba 5y ago
    You can edit your settings to make your web library publicly shareable :)
    • prepend 5y ago
      I don’t want to make it publicly shareable. I want to share the references with a group of collaborators.
• jabl 5y ago
  I used to use Mendeley, but after the evil empire bought them out and added anti-features like preventing export of the DB (or something like that, I don't remember exactly what it was anymore), I switched to Zotero. I was on the verge of exiting academic research at the time, so I don't have as much experience of Zotero, but it seems very solid. Strongly recommended! (Occasionally I wonder about how Zotero development is going. IIRC they were planning to switch from XUL to Electron many years ago, maybe that plan got shelved or they just don't have the manpower to do it..)
  • jccalhoun 5y ago
    Back in February someone in the forums wrote: "Zotero won't be moving to Electron anytime soon. We are planning to move to a more current version of the Firefox base later this year." https://forums.zotero.org/discussion/comment/376000/#Comment_376000 https://forums.zotero.org/discussion/comment/376000/#Comment...
  • robertknight 5y ago
    > added anti-features like preventing export of the DB (or something like that, I don't remember exactly what it was anymore) The application's internal SQLite database was encrypted. The user-facing export functionality is still there, as are the public APIs used to interact with the data stored online. One of the engineers involved is a friend of mine. From what I understand the change to the internal DB was an over-zealous response to GDPR concerns.
  • jptech 5y ago
    I have been and still am a Zotero user. But I found it unfortunate that back in grad school many of my peers still used Mendeley. The school library even had workshops/classes in which they taught how to use the software. I found it ironic that despite paying loads of money to Elsevier for the journal subscriptions, they were advertising their software too!
    • dredmorbius 5y ago
      In all likelihood, Elsevier were subsidising or oturight funding those classes. TANSTAFL. Especially in consumer technology "training", which is really sales-pipeline-building, and hooking addicts for life. You might find FOIAing the library or univesity interesting, for contractual relationships.
• brainlessdev 5y ago
  Zotero works with LibreOffice as well. It helped me tons while writing my thesis!
• temp8964 5y ago
  What I (and believe many others) really want is a self-hosted Zotero server. See question has been asked: https://forums.zotero.org/discussion/73721/zotero-self-hosted https://forums.zotero.org/discussion/73721/zotero-self-hoste... https://www.reddit.com/r/zotero/comments/d270kv/zotero_dataserver_selfhosted/ https://www.reddit.com/r/zotero/comments/d270kv/zotero_datas... https://github.com/zotero/dataserver/issues/105 https://github.com/zotero/dataserver/issues/105 https://softwarerecs.stackexchange.com/questions/48335/foss-and-selfhosted-alternative-to-endnote-zotero https://softwarerecs.stackexchange.com/questions/48335/foss-... https://groups.google.com/g/zotero-dev/c/9FdSz0kIG_4?pli=1 https://groups.google.com/g/zotero-dev/c/9FdSz0kIG_4?pli=1 Unfortunately, there is no officially supported way to do this. The official dataserver package does not have an instruction: https://github.com/zotero/dataserver https://github.com/zotero/dataserver There is an unofficial package from 5 years ago https://hub.docker.com/r/facciolo/zotero_dataserver-docker https://hub.docker.com/r/facciolo/zotero_dataserver-docker
  • kergonath 5y ago
    I’m in the same boat. Plus, the iPad app was not great at the time, which is very important to me (I read and annotate papers a lot on my iPad, it is an ideal device for this). I dug a bit to see if it was likely to be resolved soon, and it did not seem like it. So I find another solution, which in retrospect was a good thing since that was 5 years ago and the situation has not changed since. FWIW I ended up using Bookends, which can use iCloud for hosting and synchronisation across devices. I wasn’t thrilled initially because it’s a fairly obscure app, but both the Mac and the iPad apps are great. The developer is very friendly and reactive, and it’s been rock solid for years now.
    • temp8964 5y ago
      Is this (https://github.com/iandol/bookends-tools https://github.com/iandol/bookends-tools) the Bookends you referring to ? I don't care about citations. All I need is a PDF organizer have categories / tags and can add notes / make annotations.
      • 5y ago
• sergiomattei 5y ago
  Is anyone using Zotero as a bookmark manager for articles to read later? I’d love to try it for this purpose!
  • SkyMarshal 5y ago
    Yup, just install the browser addon and it works for this too.
  • mynameismon 5y ago
    Yup. Using the Zotero extension, it is basically one click setup with Zotero installed. Zotero automatically downloads a copy of the webpage, and pulls any associated metadata it can find. For example, I saved this for later use: https://archive.org/details/pdfy-MgN0H1joIoDVoIC7 https://archive.org/details/pdfy-MgN0H1joIoDVoIC7. Zotero pulled the names of authors, publishers and everything else it could find.
• ricksunny 5y ago
  I like Zotero and used in in producing our latest manuscript, but in Google Docs, with 140 cites it became unwieldy and would break the sync between the in-text cites in the bibliography. So I had to save new versions of my Google Doc every time I added a cite so I always has a backup to return to in case the sync broke again. I hope the Google Docs devs can talk with the Zotero devs to make the Zotero integration more airtight (I understand these issues don’t flare up as much in Word).
• bifurcations 5y ago
  Great app, but I find myself accidentally bookmarking sites via the Chrome extension with no way to undo except for manually deleting the entry in desktop. Any consumer app would've had this implemented by now but that's the tradeoff of being FOSS. https://github.com/zotero/zotero-connectors/issues/301 https://github.com/zotero/zotero-connectors/issues/301
• schleck8 5y ago
  Isn't Zotero the company providing Wikipedia's automatic citation feature? I'm pretty sure it says "powered by zotero"
• medimikka 5y ago
  Zotero is, if you're not in the market for a closed source silo like EndNote, the only game left in town. Mendeley went full on Evil, and Papers for Mac is Mac only, closed source, and missing dozens of functionalities that are absolutely a must have in academic writing and research. An absolute must have is BetterBibTex (https://retorque.re/zotero-better-bibtex/ https://retorque.re/zotero-better-bibtex/), which adds better Citekey management and, my personal highlight, "export on add" functionality. In short, everything I save into a specific folder in my library gets exported as a .bib file right away. That way I can click a button in my browser and have the citation ready in my LaTeX editor, Word, or Obsidian (https://github.com/hans/obsidian-citation-plugin https://github.com/hans/obsidian-citation-plugin) within seconds. The latest beta also adds full Markdown export for Notes. I tend to keep my notes on papers in Zotero, attached to the paper, but export them for filing in Obsidian (which I then feed into MkDocs for our work group's large repo). Unless you need Apple Pages support, which Apple keeps to itself and only sells for mighty moolah to a select few, Zotero can do anything EndNote can do, is Open Source, and with that won't drive your PI up the wall with yet another expense.
  • WayToDoor 5y ago
    > Mendeley went full on Evil Could you explain what happened with mendeley? I've been using it for a while, and didn't notice anything different really.
    • carbocation 5y ago
      They locked down the SQLite database so that you couldn't use it with 3rd party tools (such as your own commands, or to export). I am not sure if this got reversed, but at the time it was what triggered me to switch to Zotero. (Still using Zotero, which does everything I need it to.) One thing I like a lot about Zotero is that they charge a subscription once you get over a certain amount of cloud storage, which gives me more confidence that they'll continue to exist in the future.
      • kelsolaar 5y ago
        Yes, the DB was encrypted for no good reason except that locking users. Funnily enough at that point Mendeley could import from Zorero but Zotero could not import anymore. Thanks to Greydon Gilmore and GDB, I was able to get out: https://blog-academic.greydongilmore.com/phd_related/mendeley_decrypt.html https://blog-academic.greydongilmore.com/phd_related/mendele...
• dang 5y ago
  Past related threads: Zotero: Personal Research Assistant - https://news.ycombinator.com/item?id=22694891 https://news.ycombinator.com/item?id=22694891 - March 2020 (206 comments) Mendeley encrypts users' database after Zotero provides an importer - https://news.ycombinator.com/item?id=18977461 https://news.ycombinator.com/item?id=18977461 - Jan 2019 (119 comments) Zotero: An open-source tool to help collect, organize, cite, and share research - https://news.ycombinator.com/item?id=17606929 https://news.ycombinator.com/item?id=17606929 - July 2018 (163 comments) EndNote maker's lawsuit over open-source Zotero dismissed - https://news.ycombinator.com/item?id=646121 https://news.ycombinator.com/item?id=646121 - June 2009 (6 comments) GMU sued for Zotero - https://news.ycombinator.com/item?id=319975 https://news.ycombinator.com/item?id=319975 - Sept 2008 (3 comments)
• malshe 5y ago
  I am a longtime user of Zotero and a paying subscriber too. I use Zotfile extension to manage PDF files in Zotero. The best feature of this extension is bulk renaming filenames using a predefined filename format such as authors-year-article name. Most academic papers pdf files have weird names such as "1-s2.0-S0007681321001221-main.pdf". Before Zotero and Zotfile I used to manually rename them. Then I found out that Zotero extracts metadata automatically from PDF files and can use them for renaming the files. Zotfile gives you more control. Check it out: http://zotfile.com http://zotfile.com I saw dstillman has commented here. Dan, thanks a lot for your tireless work to make Zotero the best reference manager!
• westcort 5y ago
  I write a lot of academic papers and never use this kind of software. EndNote creates uneditable references and slows down Word, Zotero had some limitations after which they charge a monthly fee, and none of the reference libraries are easy to share with external clients. Most other medical/technical writers I know only use these tools as a “reference library.” It might be useful for someone writing a thesis, but almost all professionals avoid these because they slow things down, break, and require updates that cause issues. I use API requests to get formatted references direct from PubMed, and use FileLocator Lite to search multiple PDFs in reference folders with RegEx. QPDF is useful for unlocking PDFs. This system has worked quite well for me and I don’t have to worry about my data getting locked into aging or unsupported software platforms.
  • medstrom 5y ago
    What reference library is easy to share with external clients then? Also, what do you mean by "external clients"?
    • westcort 5y ago
      Clients, editors, etc. Internal clients might be an editorial department within a holding company that works across agencies, for example. I know I am getting downvoted, but it’s a reality that these systems have caused issues for companies like mine and have not been widely used in professional publishing, mostly due to interoperability issues.
    • westcort 5y ago
      Zipped folders of PDF files sent via e-mail.
      • cycomanic 5y ago
        Sharing zipped files of PDFs amongst people is quite possibly a copyright violation. Do you have distribution licenses for all the material you ar referencing?
• criticaltinker 5y ago
  This looks really cool, but apparently it relies on a web service to extract pdf metadata: >* The Retrieve Metadata feature uses a Zotero web service to find item metadata. The Zotero client sends the first few pages of text from the PDF to the web service, which uses a variety of extraction algorithms and known metadata from Crossref, paired with DOI and ISBN lookups, to build a parent item for the PDF. The Zotero lookup service doesn’t require a Zotero account and doesn’t log any data about the content or results of searches.* Does anyone know of open source alternatives which are offline friendly? I’ve tried tesseract and was impressed but the layout analysis and OCR made enough mistakes that tasks like bibliography parsing became considerably more difficult.
• lsiebert 5y ago
  It's good to see this is still around, I was using it in the early 2010s while working in a county health department.
• dfraser992 5y ago
  No one has mentioned iLibrarian yet. No idea how its feature set compares to Zotero or Mendeley (I haven't used them much as I found them annoying in some ways) but there is a free self hostable version as well as the SaaS product. It is sufficient for managing my archive of papers. https://i-librarian.net/ https://i-librarian.net/
• theteapot 5y ago
  I heard an article on the radio the other day (BBC) about some researcher developing meta data standards to embed bibliography data into PDFs. Basically stash the relevant refs from your bibtex (or other) database into the PDF in a machine readable way and develop open source tools to parse that and allow navigation to online or local sources. Seems like a pretty good idea. But I can't remember who it was / what it's called. Anyone?
  • augmentedtext 5y ago
    Hi, that was Vint Cerf and me, Frode Hegland. The project we talked about is called Visual-Meta. You can read about it here: https://visual-meta.info https://visual-meta.info or contact me with any questions: frode@hegland.com Thanks for listening! :-)
    • nanna 5y ago
      Sounds great! Curious to hear why you're basing the standard on BibTeX rather than BibLaTeX? Seems like a step backwards given how many more types the newer standard supports
• account-5 5y ago
  I wouldn't say I'm a power user but Zotero is amazing. It loads my university citation style no hassle, has a browser plugin which works pretty good. Ive never managed to get the Zim-Wiki plugin to work though. All in all an excellent piece of software.
• NmAmDa 5y ago
  The best thing about zotero is that becuase it is open source, you xan customize it a lot. You can even add sci-hub addon that lets you get the pdf from sci-hub for non open source sources. So if I 'm interested in a paper for reading, citation or anytjing else I just add it using one click (using browser extension) then it is ready for reading. I can do bibrex (using the addon). I can use zotfile which give much functionality, I add iPAD sync and highlight the paper and then extract that to zotero. Sci-hub addon of course ia not even listed or recommended by zorero community (for obvious reasons) but this mix is very good punishment for elsevier for all the horrible things they do to science. And how even their Mandeley is evil now.
• RhysU 5y ago
  I miss citeulike. I used to pay for their upgraded service.
• hardlianotion 5y ago
  This is pretty timely. I was a big user of Papers 3, but I refused to "upgrade" to the Readcube Papers 4 version, as it switched to a subscription model that does nothing for me. Papers 3 just about still works on my comparatively up to date version of OS X, but it refuses to upload some flavours of pdf and hard errors more frequently than it used to. So I have been eyeballing Zotero, and a little put off by possible migration snags. Has anyone performed this migration? What was the outcome?
• oliverulerich 5y ago
  Before the beta version with PDF reader & annotations, the best one was Citavi (https://www.citavi.com/en https://www.citavi.com/en) - which is still better for large projects.
• jlduan 5y ago
  It seems Zotero still doesn't support 3rd party cloud service (Dropbox, Google Drive, iCloud etc). I really recommend Paperpile, especially its Chrome extension. In my opionion, nothing beats Google Docs on collaborative writing.
  • BostonEnginerd 5y ago
    I believe that they support WebDav. https://www.zotero.org/support/kb/webdav_services https://www.zotero.org/support/kb/webdav_services You also have an option to use the Zotfile extension to sync with other services.
  • d4rkp4ttern 5y ago
    Agree on Paperpile as some others have commented. Dead simple to use. For annotating PDFs nothing beats handwriting, so for that I use iPad 12.9” plus GoodNotes app.
• stereoradonc 5y ago
  Paperpile is a good alternative. I don't mind paying for them, though only hitch is that they are dependent on Google Drive alone to save your papers. Not technically open source, but they have come a long way with exciting features on the roadmap.
  • jinto36 5y ago
    Presumably there's no way to use Paperpile "offline"? The classic example of editing a manuscript while on a plane is something that does happen.
• leetrout 5y ago
  Tangentially I made a Discord server called Awesome Knowledge Management https://discord.gg/XPNeDSQE2j https://discord.gg/XPNeDSQE2j Inspired by the "who wants to collaborate" post this weekend https://news.ycombinator.com/item?id=29759115 https://news.ycombinator.com/item?id=29759115 If the folks interested in Zotero and similar products would like to share their experience and also chat about any other similar knowledge management tooling please come join us!
• Ostrogodsky 5y ago
  I love and I use exclusively Linux but sometimes I despair: > How do I install Zotero? Mac Open the .dmg you downloaded and drag Zotero to the Applications folder. You can then run Zotero from Spotlight, Launchpad, or the Applications folder and add it to your Dock like any other program. After installing Zotero, you can eject and delete the .dmg file. Windows Run the setup program you downloaded. Linux Download the tarball, extract the contents and run zotero from that directory to start Zotero. For Ubuntu, the tarball includes a .desktop file that can be used to add Zotero to the launcher. Move the extracted directory to a location of your choice (e.g., /opt/zotero), run the set_launcher_icon script from a terminal to update the .desktop file for that location, and symlink zotero.desktop into ~/.local/share/applications/ (e.g., ln -s /opt/zotero/zotero.desktop ~/.local/share/applications/zotero.desktop). Zotero should then appear either in your launcher or in the applications list when click the grid icon (“Show Applications”), from which you can drag it to the launcher. Ehhh, I am not doing all of that. Wait, there is hope, it also says: > Debian/Ubuntu-based Distros > A longtime community member maintains zotero-deb, a lightweight wrapper for > the official tarball. Let's go there! "PSA I'm in the process of transferring the hosting of these packages to the Zoero organisation. Until that is done, the following options are available: download from this repo (re)install using curl -sL https://github.com/retorquere/zotero-deb/releases/download/apt-get/install.sh https://github.com/retorquere/zotero-deb/releases/download/a... | sudo bash caveat: github has made recent changes to how they're hosting release files, which triggered a long-standing bug in apt. If you hit this problem, see this thread for a workaround. download from sourceforge (re) install using curl -sL https://downloads.sourceforge.net/project/zotero-deb/install.sh https://downloads.sourceforge.net/project/zotero-deb/install... | sudo bash caveat: sourceforge uses a mirror system that updates haphazardly and which may redirect you to a mirror that is down. If you get errors, try again in a few hours."
  • g8oz 5y ago
    Seconded, some effort by the core team towards packaging Zotero in a deb would be very welcome.
    • nerdponx 5y ago
      RPM would be nice, too. But maybe that's too much to ask for... Alternatively, what about AppImage? At least that will run "everywhere".
• mastercheif 5y ago
  What makes this different than Devonthink other than the citation management?
  • cxr 5y ago
    Zotero has a Wikipedia article about it and the other thing doesn't.
• sorokine 5y ago
  Zotero is a great tool for references. I am using it for 10+ years mostly for research papers in LaTeX+bib but also for things like "Read It Later" and notes. I find it more straightforward to use than EndNote or Mendeley and Zotero works perfectly fine with my library of about 7K entries. Also it has a useful feature that lets you save your PDFs on a WebDAV server of your choice like pcloud.com or self-hosted.
• Gatsky 5y ago
  I have tried Endnote, Mendeley, Paperpile, Sciwheel and Zotero (back when it was firefox only, which was a long time ago). I currently use and pay for Paperpile. I found the user experience to be the best for my purposes, mainly the ease of importing articles. The word plugin is hassle free as well. They seem to be pretty competent developers eg Mendeley’s iphone app wouldn’t sync properly for literally years, whereas Paperpile’s app was good from day one. The downside of Paperpile is lock-in to the Google ecosystem (only works on Chromium browsers, although firefox and safari support is coming). There is also no quick way to tag or categorise papers at the time of import from the web, you need to go to the app. Sounds like Zotero is pretty good now though, might have to check it out again.
• austinjp 5y ago
  Just another user here, sharing some tips: Zotfile allows automatic renaming of attachments, which includes moving the PDF file to a different folder. This means my zotero account still has plenty of free storage, while the space-consuming PDFs are stored in my university's effectively limitless cloud drive. I use Recoll to fuzzy-search the text of the PDFs, or just pdf2text piped through grep for simpler searching. Recoll is great, it's here: https://www.lesbonscomptes.com/recoll/ https://www.lesbonscomptes.com/recoll/ Like many others, I write docs in markdown and use pandoc and citeproc to render to Word, then libreoffice to convert to PDF since it reliably retains the formatting from a lightly-styled Word template. With citation style sheets I can be reasonably confident that citations and references will automatically take care of themselves - being tweaks for edge cases. I use pp to pre-process the markdown, mainly to allow "includes" so I can write chapters/sections as separate files then combine them. All using a horrible render.sh script that I copy into every new project and tweak as required :)
  • maweki 5y ago
    I'd like to additionally suggest syncthing to sync the PDF folder and, as you suggested, use the free account only for the metadata. Works like a charm and I have all my literature synced up.
  • jsilence 5y ago
    "Zotfile allows automatic renaming of attachments, which includes moving the PDF file to a different folder. This means my zotero account still has plenty of free storage, while the space-consuming PDFs are stored in my university's effectively limitless cloud drive." Wow, did not know that. Have to test this! Thank you!
• smukherjee19 5y ago
  As a grad student, Zotero is a lifesaver! Thanks to the people developing it! I use Google Drive for my pdf storage using some Zotfile acrobatics (awesome plugin btw) to manage my actual pdfs. I plan on switching to Zotero's cloud storage to support development as soon as I can. That being said, I wish I had a nice workflow for reading papers on my iPad like I do on PC (Windows specifically, I know there are software for the Mac/iOS ecosystem but I don't have a Macbook so...): Open Zotero -> double-click on the paper -> Bam, the pdf opens in Acrobat where I can highlight and annotate, and save to pdf directly for future use. The closest I got to this on iPad was to use the Zotfile plugin and use the Send to Tablet feature as described here [0], and opening and annotating the pdf on iPad. Another interesting workflow seems to be using Obsidian to store the relationships between papers using annotations and highlights from them [1]. Another way to do this would be LiquidText but I paid 20+ USD separately for both the iPad and Windows Store versions, and it asks me to pay up again so I don't know what's up with them... Still, I hope Zotero keeps being developed as it's the best, and perhaps the only open source research management software out there. [0]: https://www.youtube.com/watch?v=e7novaC_O_Y https://www.youtube.com/watch?v=e7novaC_O_Y [1]: https://www.youtube.com/watch?v=_Fjhad-Z61o https://www.youtube.com/watch?v=_Fjhad-Z61o EDIT: Added clarification of OS I am using.
  • complex1314 5y ago
    Did you try this https://www.zotero.org/support/ios_beta https://www.zotero.org/support/ios_beta? Works great for me.
    • smukherjee19 5y ago
      Ah, I have heard of it! Unfortunately it seems the slots are filled so I am waiting for the final version. Hope the iOS version fixes my itch!
  • maCDzP 5y ago
    I use Zoteros cloud service and the PaperShipapp. It works really good even though the app hasn’t been updated in a while.
• solarkraft 5y ago
  I just want something where I can import stuff (most importantly web pages, pdfs, epubs), read (on my e-reader), mark things/take notes, search and turn highlights into citations. The desktop version of Citavi and Zotero seem extremely overloaded. The web version of Citavi is the closest to this I've seen (it has a mode for highlighting), but it still absolutely sucks. Maybe I don't get the hang of how real researchers or scientists do things, but so far what I mention above is the core of what I really need (mainly for personal research, but also the limited amount of scientific writing I've done). I read about Zotero theoretically supporting these features, but when I last checked it out (about half a year ago) it looked antiquated, seemed to do a lot of things I don't care about and made the things I want to do so hard I was immediately disappointed and stopped bothering. Are there any products (preferably FOSS, of course) that cover my use case? Is it possible with Zotero after all? I have tried Worldbrain Memex, but it also has such cumbersome UX it's not worth using.
  • jsilence 5y ago
    As a counterpoint to your sentiment: I am really glad Zotero devs are not spending any time on polishing the UX. I loathe modern user interfaces where a lot of functionality is hidden just for the looks. Zotero does cover your use case very well and I don't actually see your criticism or UX concerns. For easy importing of books and papers use the magic wand icon in the tool bar. This allows you to import metadata via ISBN and DOI. Use the FF plugin for importing web pages. Tags allow you to cluster entries together. On the right side it is possible to connect items that have a direct connection. Double click on Pdfs to open them in a Pdf reader that can highlight and annotate. Save the file and use the Zotfile plugin to extract the annotation into notes. Zotfile and Zutilo are recommended plugins.
• ashton314 5y ago
  Zotero is amazing. The iOS beta makes reading PDFs in your library pure bliss. I could have self-hosted a file store, but I went with the paid one instead to send the devs a little love. (And money.) They’re sooooooo awesome. Super responsive when I’ve asked questions, and the beta has been rock solid. (That said, any devs here? Why haven’t you shipped this epic app?) Deep appreciation for excellent, open-source software that is really polished.
• nerdponx 5y ago
  Has there been any progress on self-hostable Zotero Storage? I got kind of frustrated being forced to rely on their sync hosting and haven't used it in years. Edit: it looks like they support WebDAV, which I now have set up but didn't in the past. Maybe I can try it again using that protocol.
• de6u99er 5y ago
  Again?
• erie 5y ago
  Yes, it was pure joy when-in 2009- Zotero beat Reuters: A Virginia Circuit Court judge dismissed a lawsuit this morning against George Mason University’s Center for History and New Media. Thomson Reuters Inc. had sued the university in a Virginia court in September for at least $10-million in damages, claiming that Zotero, a free software tool created by the university, made improper use of the company’s EndNote citation software. Zotero is a plug-in for the Firefox Web browser that is designed to help scholars store and organize their online research. The program, which could convert EndNote files, had been downloaded over one million times by September. George Mason University said in November it had not renewed a site license for EndNote, and would not make any changes to its software. A spokesman for the university confirmed the case had been dismissed but declined to comment further. Officials at Thomson Reuters were not immediately available for comment on the dismissal. — Marc Beja https://www.chronicle.com/blogs/wiredcampus/judge-dismisses-software-licensing-case-against-george-mason-u https://www.chronicle.com/blogs/wiredcampus/judge-dismisses-...
• alanh 5y ago
  Is there an easy way to "share" a URL from iOS/iPhone to Zotero? They have an iOS app in closed, full beta, with an App Store version apparently coming soon. In the meantime, are there solutions?
  • dstillman 5y ago
    You can paste the URL or an identifier (e.g., DOI) into the save page [1], or even create an iOS shortcut that encodes the current URL into the 'q' parameter for that page. Historically the solution was to use the bookmarklet [2], but you might need to disable "Prevent Cross-Site Tracking" in the Safari settings for that to work reliably. But yes, the beta iOS app [3] supports full saving of metadata and PDFs via the Share sheet. (Disclosure: Zotero dev) [1] https://www.zotero.org/save https://www.zotero.org/save [2] https://www.zotero.org/download/bookmarklet https://www.zotero.org/download/bookmarklet [3] https://www.zotero.org/support/ios_beta https://www.zotero.org/support/ios_beta
• fjfaase 5y ago
  I am doing research on a subject where almost all of the source material is in printed material, meaning that I have a lot of scans (photographs actually) that I want to reference. At first, I just extracted the facts, but then I discovered that I have to beter track the sources. What I would like is a process where I transcribe parts of the images, turn those text in some semantic format, describing the facts, and then have a tool to combine these facts and to resolve conflicts, because, yes, the source materials contain errors. I have thinking of developing my own tools for this, but if I could use some existing tool that would be nice.
  • jabl 5y ago
    The same people developing zotero are also developing a tool called tropy that might be partially what you're looking for: https://tropy.org/ https://tropy.org/ Disclaimer: I have never used it myself, I'm just aware of it existing.
    • jsilence 5y ago
      This is great news! Thanks for the link!
• leonry 5y ago
  Similar to other commenters I would prefer some things over how they are done by Zotero. But what holds me back from switching to another solution is clearly the community. There are enough plug-ins to make Zotero work more as I wish and the people at the forum (https://forums.zotero.org/discussions https://forums.zotero.org/discussions) are very helpful.
• erenw 5y ago
  Pretty cool
• jrichardshaw 5y ago
  I've tried to use Zotero over the years, and I always stumble with it because it didn't have a good handling of arXiv id's. The arXiv is one of the primary way of finding papers in my field (cosmology), and I really want to support ingestion via them, looking up actual paper details from them (while retaining the arXiv id), and including them in bibtex exports. I check back from time to time, but I don't think that's massively improved, but I would be very happy if anyone else knows otherwise. Although it's gotten a little maligned here, I've actually switched to Readcube Papers recently, it supports everything I list above, and has been pretty good for everything else. It's a closed source and subscription which isn't ideal, but in the end I'm willing to pay for something that supports my workflow. I do worry a little about getting locked in, but ultimately, provided I'm willing to ditch any annotations, I think I can just export everything as bibtex and import to something else.
  • dstillman 5y ago
    Zotero has supported adding items via arXiv ID since 2018, and saving from arXiv.org since forever. There's not currently a dedicated field for arXiv IDs, but they're added to the Extra field and included in exports (and accessible however you want via Better BibTeX export). (Disclosure: Zotero dev)
    • jrichardshaw 5y ago
      Thanks, that's good to hear! I'll give it another look next time I look at switching things up.
• thenoblesunfish 5y ago
  Once I bailed on Mendeley, I considered other options, but found that most of my needs were satisfied by simply: - a canonical naming scheme for references in my single BibTeX file - a directory of PDFs using those names I have some for-fun little vim macros to e.g. use “open” (OS X) to open a PDF corresponding to a canonical reference name.
• Labo333 5y ago
  I tried Zotero and equivalent softwares (mendeley) a few times but never caught. My typical workflow involves a big gdoc that I can share with my advisor. I paste the title, year, author and number of citations (to know which articles are the most influential). And, most importantly, a link to the pdf (sometimes through sci-hub). Then I write notes under those articles, pasting screenshots of equations that I want to find easily. When I have to write my paper, and this is the only painpoint, I have to paste the titles to google scholar and copy the bibtex code. I might write a simple bot at some point to do it for myself. I'm taking every advice to improve this!
  • faustlast 5y ago
    Workflow: 1. copy doi and extract in into zotero (automatic looks for pdf). 2. better-bibtex (zotero add-on) will automatically generate the .bib entry. 3. tex editor automatically recognize bibtex entry. 4. write all the relevant stuff with proper formatting (ready for paper). 5. git and github for sharing.
    • Labo333 5y ago
      that looks very cool! I found https://gagarine.medium.com/use-sci-hub-with-zotero-as-a-fall-back-pdf-resolver-cf139eb2cea7 https://gagarine.medium.com/use-sci-hub-with-zotero-as-a-fal... to get the pdf from sci-hub\ Thanks!
• natded 5y ago
  Installing this in Ubuntu is a PITA and I always just give up. No I'm not going to start """symlink this and that""" when my aim is to save references for myself.
• todd8 5y ago
  Off topic, I suppose, but this seems like the place to ask if anyone knows how to find a book's library call number (like Dewey Decimal or LCCN) from knowing the ISBN for the book. I've played around with various MacOS apps, EndNote, and a few other programs, but I've always found the solutions awkward. Does Zotero support this functionality? All I really need is a public SQLite database of book information that contains both ISBN and Call Numbers. I have a library of (approximately 6000) books that need spine labels. Scanning ISBN's is easy with inexpensive hardware, generating barcoded spine labels isn't hard (using python + LaTeX), and applying them in an archival fashion isn't difficult (using laser printed non-acid paper and 3M Book Tape). The main difficulty is determining accurate Dewey Decimal call numbers for each book. It takes me up to several minutes per book to find this information by hand on the internet. I'm wondering if there is a way that works programmatically and is less expensive than subscribing to the the WorldCat Search API, a service that makes sense for larger libraries.