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Zotero: An open-source tool to help collect, organize, cite, and share research
- rusbus 8y agoWow what a throw back...I remember using Zotero in middle school over a decade ago. It was a great tool then, glad to see they're still going strong.
- SOLAR_FIELDS 8y agoI thought the same thing - It looks like they've come a long way since I used it eons ago.
- maym86 8y agoLooks like https://www.mendeley.com https://www.mendeley.com
- azag0 8y agoThey 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
- zouhair 8y agoIt's an Elsevier product, so no interest there. I'd rather just use JabRef http://www.jabref.org/ http://www.jabref.org/
- hyeonwho4 8y agoMendeley is supported by Elsevier, closed-source, and has premium-only features only for institutional users. Its publisher affiliation is important, when you see things like "Mendeley supports responsible sharing." Zotero is the full package, GPL, the only premium service is extra data for syncing with their server (not necessary if you only have one client). None of this Orwellian hinting about keeping researchers from using libgen.
- maym86 8y agoYeah. Was just sharing it because it's what I used 5 years ago for my PhD. Worked well at the time and I found it useful. I don't think Elsevier owned it then. Got heavily down voted so I'll take the hint :) Reading about Elsevier now and I understand the objection. Thanks. https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science https://www.theguardian.com/science/2017/jun/27/profitable-b...
- lzmartinico 8y agoBut 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)
- jccalhoun 8y agoaccording to wikipedia, zotero was first released around a year before mendeley
- th0ma5 8y agoCan 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.
- hyeonwho4 8y agoIt 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.
- tonyg 8y agoYes, 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.
- beezischillin 8y agoWe also used Zotero during our university studies for keeping track of citations. It's a great tool!
- innocenat 8y agoZotero really need more advertisement. I prefer Zotero over Mendeley, but Mandaley seems to advertise much more to university.
- msaharia 8y agoAlso, Mendeley was bought by Elsevier. Zotero is open source.
- Sol- 8y agoEven 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.
- dotancohen 8y ago> 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.zandy.app https://play.google.com/store/apps/details?id=com.gimranov.z... https://play.google.com/store/apps/details?id=computer.benjamin.zotdr0id https://play.google.com/store/apps/details?id=computer.benja... https://play.google.com/store/apps/details?id=net.ezbio.zotez https://play.google.com/store/apps/details?id=net.ezbio.zote...
- pmontra 8y agoThe site is not very clear about if it's possible to self host the server part, but hopefully the server is the PHP application at https://github.com/zotero/dataserver https://github.com/zotero/dataserver
- brailsafe 8y agoYes. You can self-host a WebDav server and easily point Zotero at it.
- deleted 8y ago[deleted]
- TeMPOraL 8y ago> 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... ;).
- PetitPrince 8y agoZotero can extract meaningful data from PDF. Alternatively, you can use the paper DOI.
- voxadam 8y agoA quick DDG search lead me to this: https://www.reddit.com/r/scihub/comments/7ilwzv/scihub_look_up_engine_for_zotero/ https://www.reddit.com/r/scihub/comments/7ilwzv/scihub_look_...
- krrrh 8y agoCan confirm, this works.
- Cenk 8y agoCitationsy works with Sci-Hub... just saying :) https://citationsy.com/blog/new-feature-citationsy-archives/ https://citationsy.com/blog/new-feature-citationsy-archives/
- bdz 8y ago
- voxadam 8y agoDocear is another interesting project. Unfortunately though, Docear isn't nearly as active as it once was. http://www.docear.org/ http://www.docear.org/
- gtpedrosa 8y agoI came in just to give a shout out to Docear as well. There is an extensive blog post comparing Docear, Zotero and Mendeley made by Joeran Beel (Docear's team)[0]. I can't recommend it enough. It helped to get the review of my MSc thesis done easily combining a mind map approach to actually cliackable pdf links (in sync in multiple pcs), all this with bibfile integration. I actually blogged about it in portuguese [1]. However due to the literary suite paradigm I would recommend Jabref (which is integrated in Docear) instead [2], if you are coming from Zotero/Mendeley, which is what I Did. Docear alone is capable of much more. I was not aware it is not really active these days. It is really unfortunate. [0] https://www.scss.tcd.ie/joeran.beel/blog/2014/01/15/comprehensive-comparison-of-reference-managers-mendeley-vs-zotero-vs-docear/ https://www.scss.tcd.ie/joeran.beel/blog/2014/01/15/comprehe... [1] https://gtpedrosa.github.io/blog/apresentando-o-docear/ https://gtpedrosa.github.io/blog/apresentando-o-docear/ [2] http://www.jabref.org/ http://www.jabref.org/
- patrickg_zill 8y agoDoes it only store the metadata or does it have the power to store the full text, whether pdf or website or other document? Could you use this like a digital "commonplace book"?
- Schiphol 8y agoYou can store pdfs and other article files, and sync them across devices. The first 300MB are free, and there are 2GB, 6GB, and unlimited-storage paying tiers.
- brailsafe 8y agoYou can also just set up a WebDAV server and sync that across devices. Works pretty damn well.
- Schiphol 8y agoHuh, that's interesting! Do you know of a blog post where this is spelled out?
- phireal 8y agoI use my Nextcloud install (since it provides a WebDAV interface). In the options under the Sync tab, I select WebDAV as the File Syncing type and for the URL I put: my.nextcloud.server.com/remote.php/webdav with the appropriate credentials. Works flawlessly.
- Schiphol 8y agoThanks a lot :)
- beeuys 8y agoActually 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.
- brailsafe 8y agoZotero 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.
- limbicsystem 8y agoZotero rocks! I encourage all my students to use it as well even though the University has a license from Endnote. Power tip: reduce the number of characters searched from the default 500000 to more like 10000 for large (>5k) libraries otherwise I find it slows down quite a bit.
- Freak_NL 8y agoIt 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!).
- est 8y agoreminds of an ancient site called diigo. Still operating.
- staamen 8y agoAlways been a very happy Zotero user throughout my degree to manage my citations. Without it writing papers would have been a much bigger headache.
- aq3cn 8y agoThis software is available in 30+ langauge, but not in any Indian langauge. I wonder why developers Ignore translation of softwares in Indian Languages. If dev team is reading this, please contact me. I would translate this software in Hindi language. Update: I wonder why this comment got downvoted any without explaination. HN is not same, as it used to be.
- Freak_NL 8y agoTranslators are welcome to help. Read this: https://www.zotero.org/support/dev/localization https://www.zotero.org/support/dev/localization
- aq3cn 8y agoThanks, I will do the the translation in my free time. I hope other people also join in.
- barry-cotter 8y agoSame 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.
- icelancer 8y ago>> 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.
- SubiculumCode 8y agoI 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.
- Freak_NL 8y agoI 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.
- black_puppydog 8y agoBeing able to quickly import literature via embedded metadata or specific extractors within zotero is incredibly convenient. They have a super simple interface to do this from firefox, but I also configured my qutebrowser via a userscript: https://github.com/parchd-1/qutebrowser-zotero https://github.com/parchd-1/qutebrowser-zotero
- zwaps 8y agoI 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.
- lvbu 8y agoYou can just all all the pdfs by "Store copy of file" option. It allows multi sect. Then you can select all of them and do a fetch metadata together.
- decasia 8y agoYour 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.)
- ekphrasis 8y agoThe 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]. [1] https://www.zotero.org/blog/zotero-5-0-36/ https://www.zotero.org/blog/zotero-5-0-36/ |2] https://github.com/citation-style-language/styles https://github.com/citation-style-language/styles
- 8y ago
- singingfish 8y agoZotero is awesome. 80% of the academic type people I've introduced it to have switched. The other 20% have Endnote stockholm syndrome.
- singingfish 8y agoIn 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.
- bede 8y agoHaving 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.
- jccalhoun 8y agoEndnote. 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.
- jhbadger 8y agoParticularly bench biologists tend to have "The only way to write a paper is Microsoft Word and Endnote". Zotero is considered a bit eccentric and using LaTeX is practically unheard of. As a computational biologist I like Zotero and LaTeX but am often forced not to use them in collaborations.
- singingfish 8y agoI 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.
- montalbano 8y ago6 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!!
- deleted 8y ago[deleted]
- lxhrstn 8y agoI 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.
- gmac 8y agoI've used Zotero for about 10 years. Its one-click citation saving is awesome. But since I am a LaTeX/LyX person, I also wrote an extension that lets Mac users automatically add newly saved citations to BibDesk: http://mackerron.com/zot2bib/ http://mackerron.com/zot2bib/
- mblode 8y agoFor my university essays, I keep my research citations in Zotero and write in Markdown using Ulysses. Then when it is ready to submit, I'll use Raphael Kabo's technique [1] to export into Microsoft Word. It is a truly simple workflow to get perfect formating with little effort. [1] http://raphaelkabo.com/blog/posts/markdown-to-word http://raphaelkabo.com/blog/posts/markdown-to-word
- telesilla 8y agoI 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.
- austinjp 8y agoGenuine question: what do you do with Word docs sent back to you as email attachments with track changes and embedded comments? I'm slowly realising that my colleagues for whom this "works" are never going to change. Our shared folders are littered with "Copy of FINAL final + comments 2.7.18-my-copy.docx.docx". It doesn't matter how slick my git + markdown + pandoc workflow is when conversations go like this: "Just use track changes." "But..." "JUST USE TRACK CHANGES."
- alexchamberlain 8y agoIs your markdown to Word reversible? If so, accept all changes, convert back to Markdown and run git diff. I guess you're losing comments though.
- austinjp 8y agoDefinitely worth a go. Comments might be extractable, I'm not familiar with docx format but it's zipped X(?)ML type data so there will be parsers. Or a conversion to an intermediate format that's more amenable to computer processing, perhaps. The problem remains in reverse, though: it's expected that I will produce Word docs full of track changes edits.
- icelancer 8y agoMy 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.
- therealmarv 8y agoUsed back in the day Zotero Bibtex export with Markdown and this workflow/template https://github.com/tompollard/phd_thesis_markdown https://github.com/tompollard/phd_thesis_markdown for my thesis. Zotero is very good (especially with extension on the browser, it's like pinning something in Evernote) and the best is: it's free.
- wycx 8y ago5 years and 7464 references later Zotero has become an integral part of my workflow. The combination of Zotero and the custom renaming of Zotfile lets me store all my pdfs in Dropbox, but sync all database by Zotero such that I can add references at work and have them waiting for me on my PC at home. I abandoned Mendeley because it would not permit relative paths, and I have not looked back.
- 131012 8y agoI loved zotfile for its feature which enable user to highlight/comment articles then import the text in notes related to article.
- degenerate 8y agoOur team switched from a custom solution to Mendeley last year instead of Zotero because Mendeley lets you highlight and add notes in the PDF, which gets shared among the whole team with those markups. Zotero didn't have that. Otherwise we would have went with Zotero.
- dstillman 8y agoIn Zotero you just do that in your PDF reader of choice. If you're using syncing, as long as the PDF reader saves annotations back to the original file, Zotero will automatically sync the updated file to other group members. The one downside of this approach is that multiple people can't modify the same PDF at the same time. The upside is that you can use whatever PDF tools you want and annotations remain accessible in the file even if you stop using Zotero, which goes with our philosophy of leaving people in control of their own data. (Mendeley stores annotations and highlights in its own encrypted database, and you can't even export PDFs with annotations in batch. If you want to get a PDF with your annotations out of Mendeley, you have to do it one file at a time.) Disclosure: Zotero developer
- degenerate 8y agoThanks for explaining how it can be achieved in Zotero. We did try this out, but just as you mentioned, the annotated/highlighted PDF changes the file. We liked how Mendeley keeps that information in a separate DB and lets you make the markups right in the app, instead of having to do it yourself outside the application. It was simply more seamless for our non-tech people.
- michaelmior 8y agoI had tried Zotero before but I stuck with Mendeley for a long time. I ended up using Zotero a couple years ago to share some references with my advisor and since then I've grown to love it. One of the nice things about it being based on Firefox is that there's a lot of extensions written for it (which IMO, are not well-advertised). The API is also great and I've been using it to automatically sync PDFs of papers I want to read to my reMarkable tablet. https://michael.mior.ca/blog/zotero-remarkable-sync/ https://michael.mior.ca/blog/zotero-remarkable-sync/
- geeio 8y agoDo you like the reMarkable tablet? I currently have an iPad Pro but I really don’t like reading PDFs on it. I’d love to stop printing out papers and an eink display would be nice. EDIT: just read your review linked in the post
- michaelmior 8y agoOne thing I'll add that has happened since the post was made is that the reMarkable team has been pretty good at churning out updates. The last firmware update adds table of contents and text search for PDFs and its incredibly fast. My two biggest annoyances are currently: 1) No web app, so the only way to export PDFs is via the desktop app which is only available for Windows and Mac. The Android app is also pretty terrible. I think not starting with a web interface was a bad decision. 2) The PDFs exported from the desktop app are huge (a PDF that started out ~400KB ended up >100MB after export). Support tells me they're working on this.
- philgooch 8y agoZotero is great, does everything except actually read your papers for you. Although, there is a tool out there now that does that.
- danielecook 8y agoI am a big fan of paperpile: https://paperpile.com https://paperpile.com I've used Endnote, Mendeley, and Zotero before and found them all to have their own issues. Paperpile is not perfect but it shines in a few places and I really like it. The chrome plugin adds an 'add to paperpile' button to places like google scholar making it easy to add citations. It also is designed for writing in Google Docs and makes it very easy and quick to add citations. For some, Google Docs may be a dealbreaker, but if you need to collaboratively write/edit a manuscript it's much better than the alternatives in my opinion (esp. because everyone can write/edit at the same time).
- innocenat 8y agoZotero also have chrome plugin that, while I don't remember it work on Google Scholar, I use it all the time on actual journal site (IEEE Xplore, arxiv, Nature, ACM, etc.)
- dangom 8y agoI'd like to switch to Zotero, but I've been using Mendeley for a good 5 years, and built a decent workflow around it. I was wondering if anyone here took the leap and made the switch, and could perhaps point out some of the biggest differences between both tools?
- tonyg 8y agoI did, just recently; the biggest difference, to me, is that you have to configure synchronisation of PDFs yourself, if you don't want to use the Zotero web account thing to do it for you. I haven't tried the Zotero account file-syncing option, myself; I just use the Zotfile extension to make it copy the files to a Dropbox folder. ETA: The firefox integration of Zotero is great, and something I missed from Mendeley. Also, I should say, before I switched to Zotero, I was a Mendeley user for about nine years, and did my PhD dissertation's bibliography using it. I'm quite confident Zotero would have been just as good.
- puzzlingcaptcha 8y agoThe ability to host your attachments (.pdf files mostly) on your own WebDAV server is very useful.
- nanna 8y agoI used Zotero through my MA and into my PhD, when I discovered and began writing in LaTeX in emacs/AucTeX instead of LibreOffice. I used the Better BibTeX plugin [0] to maintain a BibLaTeX file, but as I developed my emacs skills I moved to RefTeX. At that point I realised that my BibLaTeX file was really a mess. Better BibTeX created tons of needless double curly brackets {{like this}} in the BibLaTeX file, making searching it directly a pain. And it created lots of @misc entries, the BibLaTeX entry of last resort, when it should have made @url's and other things. Zotero has massively benefited my work, but it's also been something of a training wheel which in the longer term slowed me down. Emacs/AucTeX/RefTeX does everything Zotero does (at least according to my use) but faster, cleaner, more holistically, and with more features (eg crossref'ing entries). And two years on I'm still cleaning up that Better BibTeX's BibLaTeX file. [0] https://retorque.re/zotero-better-bibtex/ https://retorque.re/zotero-better-bibtex/ * edited because I confused AucTeX with RefTeX.
- jhbadger 8y agoI guess I don't see how you can easily add citations without something like Zotero (or its closed source equivalent Endnote). At least in my use case, I go to Pubmed and click the Zotero Chrome plugin to add the reference to Zotero. What do you do, manually enter the info?
- nanna 8y agoNah, not manual at all. I just call up RefTeX by hitting ctrl-x + (or "C-x +" in emacs parlance). This calls up a list of all possible references and a fuzzy search box which lets me narrow it down. When I've found my reference I have ten options, including: f1: Open associated pdf, url or doi f3: Insert the citation into my thesis and then be asked for what kind of note I want to add (footnote? Title? author name? Year? Just a bibliography entry?), then any text to add before the reference (eg, "This argument has been made by,"), then after (p. 67). -- This answeres your question f7: Attach pdf to email f9: Show notes, if there's an .org file of the same name. f10: Add pdf to library If RefTeX can't find my query, not only does it ask if I want to add a new one, it asks whether to search various databases for it including arXiv, DBLP (computer science bibliography), Google Scholar, Bodleian Library, HAL, Library of Congress, British Library and others. Adding entries to the database is as simple as editing a plain text file, and BibTeX provides quick shortcuts for all the different kinds of entries, checks them for you and provides a sane and customizable key. Everything is completely integrated - my writing, my pdf library, my org notes, my bibliography database, my email as well as my thesaurus (wordnut), my pdf reader (pdf-tools) and my git repo (magit). It's just brilliant. All together it makes emacs the ultimate writers tool, as far as I'm concerned.
- zip1234 8y agoI used Zotero while going through University and it seemed revolutionary at the time. There wasn't really anything else that could properly import the citation info from journals, web sites, etc so easily. Most of them you would have to type everything in manually. Zotero changed all of that and truly made it easy. Glad to see that it has kept getting better and better.
- msconnect 8y agoIt is ok not great. Lack many features. If they make app they can bring in many features from other citation managers very simple way. But all the citation managers out there half cooked softwares and so is this one. It is just a very basic tool with no features. Mendekey is better, papers is good, endnote is good but all those are expensive and not free except mendeley. So if they want it for just a regular bare minimum use tool then it is ok but otherwise power users and more trouble free versions are as mentioned above however these paid softwares also lack serious features even after paid. So you can’t expect much from free versions. Also zotero design is not sleek clean. It looks very raw and clumsy. Which can be easily improved by better interface design.
- ipstone2014 8y agopeople should try readcube.com, it's not free, but the best I can find to organize papers/references from any platform (iOS, android, pc/mac/linux).
- jknz 8y agoI use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search over the first page of each pdf (The first page of each pdf is extracted using pdftotext, but cached so it's fast). The first page of academic PDFs usually contains title, abstract, author names, institutions, keywords of the paper; so typing any combination of those will quickly find the pdf. What is particularly convenient is that no time is spent trying to organize the papers into folders, or importing them into software such as zotero. The papers are passively downloaded, and if I remember ever downloading a paper, it's one fuzzy-search away. Of course it does not solve the problem of generating clean bibtex files. [1]: the script: https://github.com/bellecp/fast-p https://github.com/bellecp/fast-p [2]: an illustration in GIF: https://user-images.githubusercontent.com/1019692/34446795-12229072-ecac-11e7-856a-ec0df0de60ae.gif https://user-images.githubusercontent.com/1019692/34446795-1... edit: The script has been moved from the gist to the public repository https://github.com/bellecp/fast-p https://github.com/bellecp/fast-p
- paultopia 8y agoThis is awesome! Interesting enhancement idea, slap a NLP topic model on top of it and explore by clusters. I'd pay for a product that did that (and if I ever find the time might try and do it myself).
- SnowflakeOnIce 8y agoThis is terrific! Thanks for sharing. fzf is a wonderful piece of software.
- sixdimensional 8y agoI love the passive nature of your workflow. I’ve always thought that, as soon as I had consumed (read, viewed, heard) some content (text, audio, video) it would be nice to have a “shadow copy” of it stored in a personal, private knowledgebase, with a simple keyword or more complex semantic search on top. Basically, a personal search engine with a passively gathered corpus of my experienced content - maybe even filtered at times as in your case where you limited it to academic PDFs (to keep the knowledgebase focused). Kind of like an extension of our human memory. Consume -> add as extension of knowledgebase -> recall. Thank you for sharing your workflow - simple and ingenious! Have you had any issues or thoughts for future enhancements? I can think of a number of other helpful things you could do with the corpus you’ve built, for yourself.
- nerdponx 8y agoZotero really needs to become self-hostable. Other than that, it's a great tool.
- Sabinus 8y agoFeature request: integration with Sci-Hub
- levesque 8y agoThat's not gonna happen, unless they dislike being sponsored/funded.
- foobarbecue 8y agoHappy zotero user for the last decade here.
- jkh1 8y agoI don't want a third party cloud-based solution and Zotero is not clear on where your data is by default. So I went with JabRef (http://www.jabref.org/ http://www.jabref.org/)
- rotskoff 8y agoI recently switched to Zotero from Papers, which is only for OS X and I needed to work on a Linux computer. After Papers was acquired by ReadCube, I was also concerned it would end up like Mendeley, which has a social network model that I don't particularly like. On the whole, the transition was pretty effortless and I am pleased with Zotero (plus the Better BibTex plugin and webdav syncing). I like having the rss feeds inside the client. The firefox add-on is far superior to the Papers version. And finally, because it's an open source project with a reasonable ecosystem, many of the things I found annoying about Papers have been solved (like customizing which fields to exclude from a bibtex export).
- phren0logy 8y agoI have been really happy with ReadCube. It's kinda clunky and awkward in some places, at least compared to Papers, but it works very well. I'm a happy paying customer.
- peebz 8y agoI've tried Zotero but have been using JabRef (http://www.jabref.org/ http://www.jabref.org/) for a good few years now and it works well for me on Linux.
- techbio 8y agoImportant supporting institutions. GUI looks like a lot of overlap with Citavi. https://www.citavi.com/en https://www.citavi.com/en Major differences seem to include cloud based Zotero's advantages for sharing, collaborating, and Citavi's better fine-grained document quote/cite tools. https://www.quora.com/What-is-the-difference-between-Citavi-and-Zotero# https://www.quora.com/What-is-the-difference-between-Citavi-...
- anfractuosity 8y agoI see references here about zotero being able to look up metadata for a pdf. I'm slightly confused what that means, is that just meta data in the pdf file, that isn't visually visible? For a while I've wanted to make something that can extract the title, authors, and bibliography visually from a pdf. Is that what zotero can do also?
- dstillman 8y agoIt doesn't use embedded metadata in the file, which is usually pretty low quality. It looks for various identifiers (DOI, ISBN) in the first few pages that can be used to retrieve high-quality metadata from external services. It also does some analysis to try to identify the title, authors, abstract, etc., and compares those against known metadata for further lookups and/or to supplement the retrieved metadata. (This is a web service [1] because of the database requirements, but we don't log any data about the contents or results of searches, and it's an optional feature.) For extracting metadata from a formatted bibliography you can use AnyStyle [2], which is a separate service written by a Zotero developer. [1] https://github.com/zotero/recognizer-server https://github.com/zotero/recognizer-server [2] https://anystyle.io https://anystyle.io
- anfractuosity 8y agoGotcha, thanks a lot for your reply!
- paultopia 8y agoI want to love Zotero, I really do. But the last time I tried it seriously, I found that: - metadata extraction/automated adding really doesn't work right with my research workflow (a lot of google scholar searches, a lot of humanities and social science sources)---lots of inaccurate or incomplete info, lots of downloading RIS files and then manually importing and separately manually importing the PDF. - documentation for things that would be useful like hooking up to academic library proxies is nonexistent. Take a look at the chain of empty links when you try to get proxy info: https://www.zotero.org/support/proxies https://www.zotero.org/support/proxies - no better bibtex for zotero 5... Although maybe this has changed recently? Which would be amazing.
- dstillman 8y ago> metadata extraction/automated adding really doesn't work right with my research workflow I'm not sure exactly what you mean, but the primary way of adding items to Zotero is with the Zotero Connector browser extension, which lets you save high-quality metadata and PDFs with a single click from a huge variety of sources (certainly including humanities sources, since Zotero was created by historians). No other tool comes close to Zotero's abilities here. Metadata quality does vary by site, though — Google Scholar specifically only provides limited metadata, so you'll often get better results by clicking through to the linked article and saving from there. We have plans for functionality to flesh out incomplete metadata retrieved from subpar sources. Zotero can also automatically retrieve metadata from PDFs you drag in, which should work for the vast majority of recent PDFs and many older ones with DOIs assigned, though that's not meant to be the primary workflow. > documentation for things that would be useful like hooking up to academic library proxies is nonexistent Current proxy documentation is here [1], and that's what's linked from the main documentation page. I've fixed the outdated page you pointed to — thanks. Note, though, that the proxy functionality is meant to work automatically for the popular academic proxies, so most people don't need to configure anything to use it. (And as far as I know other competing tools don't offer anything like this.) > no better bibtex for zotero 5 BBT has worked with Zotero 5 since last year. Disclosure: Zotero developer [1] https://www.zotero.org/support/connector_preferences#proxies_preferences https://www.zotero.org/support/connector_preferences#proxies...
- ib84 8y agoI'm a big fan of Zotero. One of the greatest features is that you can use your own WebDav-Server to store and sync PDF files. There is also this tutorial on how to install your own Zotero server [1], but I don't know how to config Zotero to use it. Anyone knows? [1]: http://git.27o.de/dataserver/about/Installation-Instructions-for-Debian-Wheezy.md http://git.27o.de/dataserver/about/Installation-Instructions...
- ib84 8y agoAssuming you managed to install your own Zotero sync server (not webdav), does anyone know how to use it with the Zotero client?
- tzm 8y agoExcellent to see and plan to try it out. I almost exclusively use DEVONThink Pro for collecting, organizing and searching local documents and Web resources. It's a key part of my research workflow, but always open to testing (or creating) improved tooling.