[HN Gopher] Zotero: Personal Research Assistant
___________________________________________________________________
Zotero: Personal Research Assistant
Author : supdatecron
Score : 505 points
Date : 2020-03-26 15:59 UTC (7 hours ago)
(HTM) web link (www.zotero.org)
(TXT) w3m dump (www.zotero.org)
| DamnInteresting wrote:
| I started using Zotero a few months ago when a major Firefox
| update rendered the Scrapbook extension non-functional. It's nice
| to be able to take quick snapshots from Chrome or Firefox and
| save them to the local document repository. I found this guide
| helpful in getting things set up:
|
| https://daily.jstor.org/how-to-use-zotero-and-scrivener-for-...
| tetris11 wrote:
| For the cloud side, there was a nice tool for linking a Google
| Drive full of PDFs with entries in your Zotero database,
| bypassing the cloud storage limits.
|
| https://github.com/mtekman/ZoteroGoogleDrive-PDFLinker-Cloud
| mcshicks wrote:
| I started using zotero after reading about it in the nytimes, I
| guess it's about 11 years ago. I'm pretty sure it's this article,
| because its the same date as the first book I added.
| https://opinionator.blogs.nytimes.com/2008/12/16/defeating-b...
|
| I mostly just used it for keeping lists of books with tags (to
| read, which library has them, on my kindle etc) and some notes.
| The bibliography report is nice. I know its is targeted toward
| research, but it really is good for people who just like to read
| books if for nothing else to remember what they have read!
|
| I think the really nice thing about it is how easy it is to add
| books. When I was using a kindle a lot, just add it from amazon.
| Recently I've been reading a lot more books from archive.org, and
| again its really easy to add it, just one click.
| abdullahkhalids wrote:
| My workflow is:
|
| 1. Come across paper pdf on the web.
|
| 2. Use Zotero firefox plugin to import it into Zotero. Zotero is
| able get citation data, and automatically exports it to a bib
| file.
|
| 3. Use emacs helm, which reads the bib file, to cite papers in my
| documents.
|
| I would have really loved to have this workflow during my Phd,
| but I was doing everything manually back then. My only complaint
| is this recent silent change in Zotero, where the exported bib
| file has entries in alphabetical order, rather than in last-added
| order. With the last-added order, when I popped open emacs helm,
| the last added paper would be on top. Now I have to search for
| it.
| tmalsburg2 wrote:
| Hi, helm-bibtex author here. Helm-bibtex has support for
| importing citations directly from CrossRef: Fire up helm-
| bitbex, type search terms (e.g., title of paper), select
| CrossRef option, select paper from search results and press "c"
| to copy BibTeX entry, "q" to close, then paste entry into your
| .bib file.
| abdullahkhalids wrote:
| Thanks for the response. I am aware of that functionality. I,
| however, usually find papers using the browser (either
| searching google scholar or on arxiv/scirate). Zotero, then
| lets me click one button (most of the time), and the entry is
| available to be cited using a nice citekey (firstauthorYear),
| and the pdf is placed in my pdf folder with the right
| filename.
|
| With all due respect to the excellent work you do (many
| thanks for that), my workflow does not require any manual
| work most of the time.
| tmalsburg2 wrote:
| I guess you have to manually export your bibliography, but,
| still, that's a pretty streamlined workflow. There's
| definitely room for improvements within Emacs.
| zneveu wrote:
| Check out the "better bibtex" extension to zotero for exporting
| to bib files, I find it helps with unicode/utf-8 characters and
| might fix that alphabetical problem.
| abdullahkhalids wrote:
| I am indeed using that. The bug reports claim it is a Zotero
| problem and not a better bibtex problem.
| gmac wrote:
| I wrote a Zotero extension many years ago when doing my PhD[1].
| Unfortunately, recent changes have broken it, I can't figure out
| what's wrong (XUL is not exactly well-documented these days), and
| the developers aren't responsive[2]. :(
|
| [1] http://mackerron.com/zot2bib/
|
| [2] https://groups.google.com/forum/#!topic/zotero-
| dev/a1IPUJ2m_...
| djaque wrote:
| Easily one of the most useful programs I've installed for work.
|
| Best feature is the web browser add-on. Can open up a few dozen
| articles during a literature search and dump all of them into
| Zotero for reading later.
| autocorr wrote:
| Zotero is simply a wonderful tool and I'm very grateful to the
| developers for it. As an academic, it is the only GUI program
| besides Firefox that I consider essential on one of my computers.
| Some of the features I enjoy:
|
| * free software
|
| * Linux and multi-platform support
|
| * browser extension "that just works" for ingesting items and
| magic lookup tool for DOIs and arXiv IDs (and I hardly ever have
| problems with the metadata)
|
| * shared group libraries for collaboration with students
|
| * offline only as well as sync
|
| * the ability to add notes, tags, and relational links between
| items.
|
| After reading about Luhmann's Zettelkasten[1] system, I've also
| had a great productivity boost by implementing a similar scheme
| in Zotero. After reading an article, I write up a summary of my
| ideas and thoughts and attach it to the article as a literature
| note. I then keep a primary repository of notes in a flat folder
| with links between them and the literature notes as my makeshift
| Zettelkasten. While not as stream-lined as some special purpose
| note taking tools, Zotero can do a pretty decent job at this
| while also having all the advantages of it's bibliographic
| system, file syncing, etc.
|
| Something I wish it had for this purpose was an "auto-complete"
| for other entries and a graphical tree viewer of relations.
| However, these aren't so bad not to have, part of the genius of
| Luhmann's original paper card notes system seems to have been the
| critical thinking required to determine which handful (1 to 3) of
| notes are most related and the serendipitous discovery process
| from having to manually walk the note files when you need to find
| something.
| souterrain wrote:
| I love Zotero for my academic work, but I'm contemplating using
| it more for less formal research as well.
|
| As Luhmann did, I'm trying to more frequently write summaries
| of articles--both actual academic articles and things like blog
| posts, news articles, even recipes. I prefer to handwrite these
| notes.
|
| For web links, I was thinking of using pinboard's caching
| feature which assigns a url like
| https://pinboard.in/cached/01234567890a/ and recording down the
| 48-bit identifier.
|
| Alas, what happens when my online service of choice fails? So,
| maybe the Zotero citation key?
|
| I'm wondering what others' experiences are with hybrid
| written/digital research workflows, and cross-referencing.
| Anyone have a "personal DOI" that works really well?
| jMyles wrote:
| Did you mean to leave a footnote to Luhmann's Zettelkasten
| system?
|
| I had never heard of it, but I found this article about it:
| https://medium.com/emvi/luhmanns-zettelkasten-a-productivity...
| elcomet wrote:
| > I then keep a primary repository of notes in a flat folder
| with links between them and the literature notes as my
| makeshift Zettelkasten
|
| Could you give more details about this ? Do you sync the notes
| to a folder ? How do you do this ? And how to you browse your
| notes ?
| Kratisto wrote:
| A college professor taught me about Zotero during my last
| semester. Awesome tool, but I wish I learned about it years
| before. I try and teach every student I meet about it.
| superlopuh wrote:
| I've started using Calibre for these purposes, saving papers from
| arXiv to it, and can definitely recommend. It takes a bit of
| manual effort to add tags to the papers, but once you have a bit
| of a collection going they autocomplete. The only downside is
| lack of read/reading/unread status, but I've hacked around it by
| rating papers and books I'm currently reading one star. I'd love
| to have an easier method for importing the papers, but not enough
| to actually have tried to write the script yet.
| loughnane wrote:
| Was looking at this just yesterday. Anyone have success self-
| hosting this?
| Cenk wrote:
| Zotero was also the first reference manger to use CSL, the
| Citation Style Language [1], now adopted by many other apps
| including Mendeley and Citationsy.
|
| [1] https://citationstyles.org
| ansible wrote:
| From the link:
|
| > _9500 free CSL citation styles._
|
| Should I ask how it has come to be that there are 9500 citation
| styles? Or will it make me angry and depressed at the lack of
| cooperation and widely accepted standards?
| ajot wrote:
| I believe most of them are the same, but with a different
| name. So, for my convenience, I don't need to think what
| citation style a journal uses, I just go and download the
| citation style with its name, even if I have the same style
| installed for another journal.
| jccalhoun wrote:
| I would guess a lot of those are duplicates but there are
| also cases where it has like APA 4 styles and one for APA5,
| and APA6, and so on.
| Flockster wrote:
| The killer feature of zotero is, that it is customizeable with
| different plugins. One very neat one is the integration with
| scihub. So you just paste in the DOI and it automaticly downloads
| the paper and adds all the metadata.
| ethanwillis wrote:
| Pretty sure I'm the author of the plugin you're talking about
| :)
|
| I did a few updates recently, but I welcome any additions/PRs
| anyone wants to send.
| rollinDyno wrote:
| Can you please link to your plugin?
| ethanwillis wrote:
| https://github.com/ethanwillis/zotero-scihub/ Here you go!
| qdot76367 wrote:
| You are amazing and have saved me so much time. Thank you
| _so_ much.
| Flockster wrote:
| Yes you are, thank you very much!
| frodo3212 wrote:
| Wouldn't have made it through my doctorate without Zotero. The
| plugins and MS Word integration made paper writing (almost)
| enjoyable! Instead of wasting hours on formatting my
| bibliography/citations, Zotero did the same work in about 2
| minutes. Kudos to the folks who maintain this incredible
| resource, and a big personal thank you!
| bredren wrote:
| Zotero's been around a while, I remember using it and its
| plugins many many years ago. Glad to see it is still kicking.
| richclominson wrote:
| This is so cool! Any plans for working on an iPhone/iPad app?
| MengerSponge wrote:
| For a version 1,2,3, etc., it doesn't need to display
| annotations or notes. Just a local browser for my library with
| tags would make my life far better.
|
| ps- fellow iPad user: check out Liquid Text. It's the bee's
| knees: https://www.youtube.com/watch?v=akEMuL4_9sk
| HorizonXP wrote:
| I used to use this almost 10+ years ago to organize my research
| during my masters. Love Zotero, glad to see it's still around!
| tobias2014 wrote:
| I've used Mendeley Desktop for some time, which I believe is very
| similar in functionality (but proprietary, yes Elsevier!):
| https://www.mendeley.com/download-desktop-new/
|
| Furthermore I think http://www.docear.org/ deserves to be
| mentioned as another free open-source solution with some
| interesting mind-mapping functionality:
| http://www.docear.org/software/screenshots/
| bovine3dom wrote:
| I reluctantly switched from Zotero to Mendeley as Mendeley has
| Android app that synchronises highlights, notes, read-progress
| etc. with the desktop version. It made reading papers on my
| tablet a delight.
| ramraj07 wrote:
| If you were on the iPhone mac side, papers had a brilliant
| solution that was appealing
| xyzal wrote:
| It should be noted that Mendeley encrypts user database,
| presumably to lock in its users: https://eighty-
| twenty.org/2018/06/13/mendeley-encrypted-db
| crazygringo wrote:
| Does it have any kind of export functionality at all?
| tpudlik wrote:
| You can export to BiBTeX (.bib).
| dajohnson89 wrote:
| Is Mendeley free? I couldnt easily tell from the website. Also,
| which is better for non-academics, who just want to organize
| areas of interest/notes?
|
| lastly -- how good is their mobile app?
| drongoking wrote:
| Mendeley and Zotero are both free, but both have storage
| limits beyond which you have to pay (Zotero is 300M, Mendeley
| is 2G). If you only store references and annotations you'll
| likely never exceed those limits, but if you use them as a
| paper archive you may. (I have a 3G archive)
| dstillman wrote:
| To clarify, Zotero's storage limit is only for syncing of
| attached files. You can use Zotero entirely offline if you
| choose, storing as much as you want, and we also support
| WebDAV or linked files (which can be in Dropbox, etc.) for
| syncing files in your personal library.
|
| (Disclosure: Zotero developer)
| djaque wrote:
| I actually specifically chose Zotero over Mendeley because
| Mendeley is owned by Elsevier. Their company has always been a
| toxic influence on publishing.
|
| Recently they even added a new dark pattern so that when you
| click the "download PDF" button on their articles it opens up a
| web app reader loaded with tracking instead of just giving you
| a PDF. You then have to spend time and click through about
| three menus to really download the PDF.
|
| It's to the point that I avoid articles published by Elsevier
| if possible. Easier in my field than others I'm sure.
| jabl wrote:
| I used Mendeley to keep track of papers during my PhD. It was
| really a fantastic piece of software.
|
| Too bad they sold out to the dark side. After they were
| acquired, I switched to Zotero, but I wasn't doing active
| research anymore by then, so I don't have as much experience
| of using Zotero. On the surface it looks pretty good though.
| Bedon292 wrote:
| I agree that Elsevier is toxic, and wish they didn't own
| Mendeley. Unfortunately, at least the last time I compared
| them, Mendeley was way better than Zotero for my personal use
| and just couldn't use Zotero. The cloud sync and sharing, the
| lit search, and all were just so much more compelling. I do
| think its been long enough I might poke at Zotero again and
| see if its caught up.
| chapium wrote:
| This is one of those cases where the "evil" side has a superior
| product. Imagine if Elsavier were a little nicer.
| bitcuration wrote:
| It'd be interesting if someone can compare it to Evernote.
| jccalhoun wrote:
| I don't think it is similar at all. I haven't used evernote but
| it is for notes and things right? This is just for citations.
| lala26in wrote:
| Zotero desktop GUI is not top notch. Feels like they stopped
| improving things in a long time.
|
| I'd rank the GUI experience this way:
|
| Paperpile > Zotero >= Mendeley
| stared wrote:
| Just curious, what is Zotero's business model (as open-source
| software for academicians)?
|
| It's most direct competition, Mendeley, has always been closed-
| source, and then got acquired by Elsevier.
|
| To make it clear: I love that Zotero is open-source. And I am
| happy it is growing (I remember the early versions, well over a
| decade ago, when I was writing my Master's thesis). I am just
| curious if they are based mostly on the storage payments, grants,
| or voluntary work.
| montalbano wrote:
| I pay them for cloud storage so that all my books + papers are
| backed up and synchronised between my computers.
|
| The free storage is pretty generous but I exceeded it after
| about 6 months of use.
| dstillman wrote:
| Early versions were grant funded, but the project has been
| fully supported by storage subscriptions -- including
| institutional subscriptions -- for years. (Lots of invaluable
| volunteer work as well, but there's a paid dev team.)
| reichardt wrote:
| One of the killer features is the multi-platform support,
| including web browsers, in combination with synchronization
| across devices and the Google Docs plugin. Makes working on a
| paper across multiple devices super easy.
| xattt wrote:
| Mendeley has this feature too. Their current desktop uses Qt.
|
| One of the other things going for Mendeley is seamless sync
| between an iPad and a desktop. Their cloud limit is 2GB free
| storage.
|
| Though Zotero has Zotfile, it's a hassle to set up tablet sync
| with an iOS device.
| jccalhoun wrote:
| I have used Zotero for years. I can't imagine writing a paper
| without it. I know some academics still do all their citations by
| hand. Fuck that shit. I can't imagine doing that - especially
| when journals often have their own citation style and if you get
| rejected by one and submit to another you may have to change all
| the citation formats.
| jszymborski wrote:
| So another great thing about Zotero is that you can share public
| bibligraphies. I've taken to making a little QR code at the end
| of my presentations that links to my bibliography (since no one
| actually reads the bibs on your last 4 slides).
|
| Here's an example from a talk I gave on Variational Autoencoders:
| https://www.zotero.org/groups/2350257/jszym_presentations/co...
| memming wrote:
| I don't use Zotero any more, but from the receiving end, the
| BibTeX it exports is terrible. Lots of non-ascii chars, bizarre
| nested curly braces, wrong capitalization detection, etc. I
| dislike collaborating with colleagues who use Zotero because it
| takes so much time to clean up their BibTeX entries.
| dstillman wrote:
| Ask your colleagues to use the Better BibTeX plugin for Zotero,
| which includes vastly better support for BibTeX-based
| workflows.
|
| Zotero's built-in BibTeX export is mostly intended as a generic
| data transfer format to other similar tools. It could surely be
| improved, and we'd be happy for patches, but contributions tend
| to go to Better BibTeX, since that's what people who care about
| BibTeX are using. (Zotero will export ASCII BibTeX if you
| choose "Western" instead of "Unicode" for the export charset,
| though.)
|
| (Disclosure: Zotero developer)
| catchmeifyoucan wrote:
| I used Zotero and their Chrome Extension when I was reading
| research papers. It automatically formatted citations, allowed me
| to add annotations and also locally saved any PDFs so I can
| access it quickly. You can also send different types of links
| such as videos, PDFs articles directly to Zotero.
|
| I'd highly recommend it!
| HamSession wrote:
| Used Zotero with Firefox plugin and word plugin. Used to use
| Mendeley, but like the open source nature of Zotero.
| SubiculumCode wrote:
| I use Zotero for my research everyday, and I am a paying
| subscriber for their storage. I love it, and it is getting
| better. I recently discovered a new feature: I received a
| notification that one of the articles I had in my library had
| been retracted! That is pretty cool! The Word/Libre integration
| is solid.
|
| When I saw Zotero at the top of HN, I suddenly wondered if they
| published a new tool. So I'm kind disappointed...but still love
| any attention they can get.
| mncharity wrote:
| Zotero phones home with perhaps more information than you
| expect.[1]
|
| By default, there's a persistent connection whenever Zotero is
| running, a request when you visit a site with a translator (eg
| NYTimes) the first time since a browser start, when you download
| a PDF, etc.
|
| I enjoyed using it, but their approach to privacy felt creepy.
| That [1] is somewhat improved... but only somewhat.
|
| [1]
| https://www.zotero.org/support/privacy#disabling_automatic_r...
| rikelmens wrote:
| It's an open source project. Feel free to fork it and remove
| parts you dislike.
| hu3 wrote:
| OP's criticism were fair enough to not deserve a dismissive
| response.
|
| I for one am thankful for their warnings.
| thoraway1010 wrote:
| Their warnings are wrong.
| pergadad wrote:
| See the response by the developer and the actual page
| linked. It seems op didn't actually read the link he posted
| and the critique was fully incorrect.
| dstillman wrote:
| (Disclosure: Zotero developer)
|
| Criticizing Zotero for privacy, of all things, is a bit
| bizarre. Zotero is an open-source project from a nonprofit
| organization with no financial interest in people's research
| data. It's designed as a local tool specifically to give people
| complete control over their data, and it's developed in the
| open. Most similar tools are proprietary programs owned by
| major publishers or analytics companies with voracious
| appetites for data.
|
| The page you linked to explains the reasons for every single
| network connection that Zotero makes and how to disable it.
| Every one enables a specific Zotero feature -- push-based auto-
| sync, fast translator updates as sites change to minimize save
| failures, open-access PDF retrieval. When we implemented
| retraction notifications, we even did it using k-anonymity to
| avoid sending up library data from people who don't use
| syncing.
|
| We're always happy to discuss design decisions in our forums,
| but I'd argue pretty strongly that privacy is one of the main
| reasons one should use Zotero, not the other way around.
| jjoonathan wrote:
| ...and you don't automatically upload pirated scihub papers
| to Elsevier cloud storage, like Mendeley does. That feature
| alone makes you a winner on the privacy front as far as I'm
| concerned!
| djaque wrote:
| Thanks for your work! It's nice to hear that Zotero seems to
| have privacy as a feature and not a side thought.
| mncharity wrote:
| Thank you for your work.
|
| > designed as a local tool
|
| Nod, a local tool. I have various expectations of my local
| tools. And if I, say, start Zotero in the morning to read a
| paper, then exit it for a meeting, then return to it
| afterward, and then exit for lunch, then at least my own
| expectations for a local tool are, for example, in tension
| with those four centralized timestamps. As are the varying
| tcp routes as I move my laptop among buildings. As is the
| request when I surf to the NYTimes during lunch.
|
| So what does privacy best practice look like? One comment
| here suggests the ability to fork and edit the code. Another
| notes the linked documentation, and being more ethical than
| Elsevier. The linked page notes the existence of scattered
| opt-out options. And also "You can avoid these requests by
| keeping Zotero open while you browse the web."
|
| My own understanding of privacy best practices, includes data
| exposure being opt-in rather than opt-out, and those privacy
| preferences being easily seen and changed in one place. My
| impression is Zotero doesn't do these.
|
| And that's just Microsoft-style privacy practice. It would be
| even nicer to have knobs, like "check for updates every
| <start/day/week/...>".
|
| > Criticizing Zotero for privacy, of all things, is a bit
| bizarre.
|
| I'd be fine with "we have limited resources; know privacy is
| important; are improving; know we have work to do to
| implement best practices, are working towards it".
|
| But my own fuzzy long-term impression has been, that such
| recognition has not been proportional to the potential degree
| of privacy exposure.
| dstillman wrote:
| I think it's important to look at these things in the
| context of the features they're enabling and user
| expectations. The fact that Zotero is a local,
| configurable, open-source tool is what gives you complete
| control over it, but it's not just a local database. It's
| deeply connected to a world of constantly changing
| websites, metadata sources, and services, and using most of
| Zotero's features implies relying on those things. If you
| want to save metadata from a website, Zotero might need to
| retrieve metadata from Crossref. If you want it to find an
| open-access PDF, it needs to connect to an online database
| to check for one. And if you want saving to continue
| working as sites changes, it needs up-to-date translators.
| From a normal user's perspective, the alternative is just
| Zotero not doing the things they downloaded it to do.
|
| > My own understanding of privacy best practices, includes
| data exposure being opt-in rather than opt-out
|
| Surely you don't expect software to default to not
| receiving updates automatically? As the linked section
| says, if you disable translator/style updates and don't use
| auto-sync, there won't be a persistent connection. But if a
| high-profile site breaks and we roll out a fix, the longer
| the delay the more people will just get an error trying to
| save.
|
| > those privacy preferences being easily seen and changed
| in one place
|
| We document every single network request that Zotero makes.
| Expecting them to all be configurable in one place in the
| software just isn't reasonable. Normal users think of
| features, not HTTP requests, and auto-sync doesn't have
| anything to do with translator update checks.
|
| > I'd be fine with "we have limited resources; know privacy
| is important; are improving; know we have work to do to
| implement best practices, are working towards it".
|
| OK, but I'm not saying that. I'm saying we consider privacy
| in all our decisions and believe we've made the right calls
| (and, for what it's worth, I can't recall a single
| complaint about our approach to privacy in many years). If
| you disagree with a specific decision, that's fine -- come
| to the forums and we can discuss. But let's be clear about
| the features that would break for users as a result.
| karmelapple wrote:
| Zotero's privacy features even extend to where data is
| stored: you can bring your own WebDAV server [1] and have
| Zotero store data there.
|
| [1] https://www.zotero.org/support/sync#webdav
| [deleted]
| jmiserez wrote:
| To be fair, that's a pretty nice link, not many companies
| provide such an overview. And most (all) of those features are
| useful things that you'd probably actually want to enable in
| daily use.
|
| And Zotero _can_ run completely offline, without an account.
|
| Now compare that to Zotero's biggest competitor:
| https://www.mendeley.com/terms/privacy
| mncharity wrote:
| Indeed. There does seem an issue of what baseline to use.
| Elsevier isn't usually thought of as a useful ethical
| baseline, but here it's a displaced competitor. Companies
| embed a variety of telemetry. And while much open source
| doesn't, some does, and this is perhaps increasing. And yet,
| if say Firefox always maintained an open but empty connection
| to mozilla, would it be adequate to suggest "well, no, that's
| not under privacy preferences, but it's documented on our
| privacy web page, and can be disabled by editing
| about.config.mumble"? Perhaps with the shift from desktop to
| phone, expectations of what it means to be local are
| changing? "Your core data is local, not hostage", but now "of
| course the app chats on the web... doesn't everything?"?
| jmiserez wrote:
| Well Firefox actually does (Web Push API):
| https://support.mozilla.org/en-US/kb/push-notifications-
| fire...
|
| > _Firefox maintains an active connection to a push service
| in order to receive push messages as long as it is open.
| The connection ends when Firefox is closed._
|
| I see what you're getting at, but I think the harshest
| criticism should be reserved for the worst services: those
| that actually hold your data hostage, don't provide an
| export functionality and use your data in all sorts of
| unethical ways.
|
| Organisations that actually honestly do value privacy and
| try to make an effort to get it "right" should be given the
| benefit of the doubt and constructive criticism, as they
| might actually listen. In many cases the feature may simply
| be driven by convenience and the competition (e.g. cloud
| storage, accounts, sync), and having a toggle for those is
| the best you can do if they want to stay relevant. In other
| cases the privacy issue may have simply been overlooked and
| the feature is improved (IIRC Mozilla has had a few of
| these).
|
| Maybe a big red "offline-only" toggle would be great, but
| the absence of that button does not in my eyes disqualify
| Zotero from being a great offline solution.
| mncharity wrote:
| Wow. And agreed. One question, re "being a great offline
| solution", in what sense offline? Able to work without
| net?
|
| Thinking about dstillman's reply, I was thought-crawling
| towards a "local/remote vs online/offline" distinction.
| So Zotero would be local but always online (if net is
| available). Versus my expectation that when using only
| local resources, a local tool will be offline.
| mfsch wrote:
| I've recently started a little project for my own reference
| manager. Since I end up writing papers in Latex, I want my bib
| file(s) to be the ground truth and I'm slightly obsessive about
| things like consistent capitalization and author names. I'd
| rather not fight my reference manager to eventually produce the
| bib file I want if I can just create that bib file in the first
| place.
|
| Everything I want from a reference manager can be done in a
| relatively simple command line tool with an interface similar to
| beets. Only the extraction of DOIs from PDFs looks like it will
| have to be a bit hacky, but if `ref im article.pdf` works for 90%
| of articles and asks me to provide the DOI for the other 10%,
| that's good enough for me.
| dotdi wrote:
| Also chiming in to say I used Zotero for my Master's thesis and I
| was happy with it.
|
| With some plugins (I don't remember exactly) I had a very nice
| pipeline of "find paper on the interntet" -> Zotero ->
| automatically updated .bib -> trigger rebuild of Latex document
| to PDF -> automatic reload in PDF viewer.
|
| The UI is somewhat dated but the functionality is great. Nowadays
| I would probably choose Citationsy, maybe only because I find the
| UI more aesthetically pleasing.
| Freak_NL wrote:
| Used it for my Master's thesis in 2009 (with LaTeX via
| xelatex), for my wife's Master thesis in 2011 (idem), and now
| we use it to keep a catalogue of the books we own (just a small
| home library of about a thousand titles). For the latter Zotero
| is also great because of its integration with on-line library
| catalogues. You just type in the ISBN number in the magic box,
| and the book's metadata is there -- in any language!1 Mostly
| just a few tweaks to the data are necessary, but it works
| rather well.
|
| 1: Tested with English, Dutch, German, and Japanese novels.
| cproctor wrote:
| Pairs well with a USB barcode scanner.
| [deleted]
| pks016 wrote:
| Same here. I used it for my first Master's thesis(in biological
| sciences). I could not make Mendeley work with Word. Zotero
| works great for writing thesis and research paper with Word.
| jszymborski wrote:
| It also plays well with Latex :) There's a BibTeX output
| style that works really well.
| sidpatil wrote:
| > The UI is somewhat dated but the functionality is great.
|
| I like Zotero precisely _because_ of its UI. It 's efficient,
| and reminds me of the Firefox bookmarks manager.
|
| In fact, I wish I could replace or merge Firefox's bookmark
| manager with Zotero, so I'd get the best of both worlds.
| andrepd wrote:
| Firefox's bookmark and history manager is atrocious x)
| Reminds me of IE5 or something like that.
| jmiserez wrote:
| Zotero is/was a XUL application, and the whole application
| used to (also) be a Firefox plugin. So the similarities are
| not unexpected.
| jdsalaro wrote:
| I did the same but with JabRef, it's a great and simple piece
| of battle tested software. Highly recommend it.
| 131012 wrote:
| I highly recommend the zotfile plugin! In itself, this plugin
| made zotero more interesting than the competition.
| MengerSponge wrote:
| Zotfile + Better Bibtex is the ticket for me
| boyband6666 wrote:
| I don't debate these make it better, but it doesn't seem
| like they should be required - most of the features are
| pretty standard!
| chispamed wrote:
| I use Zotero in combination with the Google Scholar browser
| plugin which let's you download citation files on most pages
| far more easily than those pages themselves allow you to. I can
| highly recommend this setup
| generatorguy wrote:
| I've been using http://www.qiqqa.com/ for 8 years and it does a
| fantastic job of organizing my PDFs and managing citations. It
| can do cloud based shared libraries as well.
|
| for me the killer feature is that it makes all the PDFs full text
| searchable so it is like my own personal google where the links
| never break and the content is all relevant.
|
| Highly recommend!
| SubiculumCode wrote:
| So does Zotero.
| generatorguy wrote:
| great! good to have an alternative to qiqqa in case it
| disappears, although it looks like qiqqa has killed their
| cloud libraries and gone open source. I found qiqqa after
| google desktop was EOLed.
|
| I have been quick to recommend Qiqqa whenever it seems like
| it might be a useful tool but I never really saw those
| comments get much traction - maybe because everyone was
| already using zotero?
| fatihbaltaci wrote:
| I'm using Zotero with Yandex WebDav and it's pretty amazing. But
| there is no official iPad/mobile application. Are you planning to
| release a mobile application?
| RMPR wrote:
| I use it to write my master thesis, for my not so conventional
| setup, (using markdown and pandoc) I find that it integrates
| nicely.
| ntnsndr wrote:
| Big thank you to the Zotero team (@dstillman) for your ongoing
| work, particularly the much improved web interface. One of my
| favorite features is to easily share a URL of a Collection with
| someone interested in the subject.
|
| My setup: writing in Emacs with markdown, export with pandoc,
| which grabs Zotero's .bib file made with the Better BibTex
| plugin. Works really smoothly, though takes a little tinkering to
| get it set up on a fresh rig.
| Woetoewoetoe wrote:
| When you import a work into your bib, always check if it got the
| right data! Sometimes it categorizes something as the wrong type
| of file, or it wil even implement the data of a whole other
| article. This can make it impossible for you to find the data
| back when you actually need it.
| elcomet wrote:
| I've been using Zotero for a few years and I really like it.
|
| I'm using my own nextcloud storage to get more than the 300Mb
| free storage on zotero cloud.
| beckingz wrote:
| This would have been extremely helpful when writing my book.
| boromi wrote:
| Anyone else here who only uses Jabref?
| alfla wrote:
| used jabref myself a lot, mainly because it's easy to
| understand how it works (all state is in your .bib files).
| never really missed any features.
| gtpedrosa wrote:
| I've tried Mendeley, Zotero and Jabref and stuck with Jabref
| for my masters thesis. Couldn't recommend it enough, even
| though haven't given Zotero a serious try.
|
| Synced bibtex and pdfs folder in linux and windows with
| dropbox, worked like a charm.The best part was configuring it
| based on this blog post
| (http://griechenzicken.blogspot.com/2011/10/configuring-
| jabre...) and making pdf links work on both machines. I wrote a
| blog post about why Jabref, but unfortunately it is in
| portuguese (https://gtpedrosa.github.io/blog/gerenciador-de-
| refer%C3%AAn...).
| boyband6666 wrote:
| I have used Zotero for my [part time] PhD and found it a great
| tool (I submitted last week). Whilst I love it, its a bit cranky,
| and it's a shame it doesn't have things that would clearly
| elevate it to the level of (or beyond) others like endnote and
| the elephant in the room of Mendeley: - doesn't play nice with
| cloud storage - seems you should be able to just pick your cloud
| provider and let it sync up. Instead if you try and use cloud
| storage it'll most likely corrupt your library - because of the
| above unless using their storage, it's hard to make work accross
| multiple computers (and never even tried on my ipad, which is a
| shame) - can't export a reference pack - interface is dated. I
| don't mind, but suspect it is intimidating to less technical folk
| and a bit of a barrier to entry (Mendeley is much more
| accessible) - does require plugins and fiddling to get the most
| out of it, some of which seems unnecessary (why are they not in
| the main program?
|
| Still, I've no regrets in choosing it in 2013, and think it's a
| fantastic piece of software. Hopefully it keeps on developing,
| and becomes the de facto standard :-)
| fjfaase wrote:
| Does it also have support for managing scans/photographs? I have
| about 10 Gbyte of images with respect to a research project about
| art works. The images also contain scans of materials. I would
| like to extract facts from these documents and maintain a link
| between those links and the scans. This means being able to
| annotate a part of an image, which for example is a text with an
| illustration or a mentioning of a certain art work.
| jabl wrote:
| The same people doing zotero have another project
| https://tropy.org/ which might be what you're looking for?
| (Disclaimer: I haven't used tropy personally)
| etaioinshrdlu wrote:
| It's shocking how many Git repos are used to build this project.
| It seems unnecessary. Personally I find the ability to make
| atomic commits across different parts of a project very handy.
| Don't understand the drive to break it into so many parts.
| dstillman wrote:
| Mostly historical. Zotero began as a Firefox extension, with
| separate Firefox extensions for the word processor plugins, and
| later added a standalone app that used the same codebase. Since
| Firefox discontinued support for XUL extensions, there's only a
| standalone app and the lightweight browser extensions now, but
| we haven't gotten around to merging the various build repos. We
| know it can be a pain to build, though, so streamlining this is
| planned.
|
| But it's also just a huge ecosystem with parts that are used
| and developed independently. E.g., "translators" for
| save/import/export are used in both Zotero and in the Node-
| based translation-server (used by Wikipedia and others), and we
| can give commit access to those separately from the core code.
|
| (Disclosure: Zotero developer)
| egberts1 wrote:
| No private storage repository support?
| zneveu wrote:
| I use this all the time, it's a great way to collect papers about
| different topics and easily add them to writeups. The option to
| keep a bibtex bibliography updated in real time is especially
| helpful. All it takes to add a new source is a single click on
| Firefox and then just cite in latex/docs/word.
| dang wrote:
| A thread from 2018: https://news.ycombinator.com/item?id=17606929
|
| A little bit from 2008:
| https://news.ycombinator.com/item?id=319975
|
| Related from last year:
| https://news.ycombinator.com/item?id=18977461
|
| (Links are for the curious. Reposts are fine after a year:
| https://news.ycombinator.com/newsfaq.html)
| pkilgore wrote:
| I used this to research and write what was essentially my thesis
| graduation requirement from law school in 2012. Good tool, I'm
| happy more people are finding out about it.
|
| It's up there with calibre in terms of "meh" UI but just
| excellent functionality.
| osrec wrote:
| I had a quick look at Zotero's github but couldn't quite work out
| how they render their desktop UI - is this an electron-style app
| or a browser extension of some sort?
| OJFord wrote:
| I haven't used it in a couple of years, but then it seemed to
| be using Qt/GTK/something.
|
| I believe there is a browser extension too, but the main
| program is (was) a non-electron stand-alone deal.
| gmac wrote:
| It's XUL. It used to be a Firefox extension, before Firefox
| changed how those work.
| mooneater wrote:
| The magic import is great, but I wish it understood links from
| more sources, including https://www.semanticscholar.org/
| KaoruAoiShiho wrote:
| Ahh darn I was hoping this would be an AI thing that collects and
| highlights research for you.
| metreo wrote:
| I've used this for years, it's one of the first applications I
| add to a new build. Keeps all of my reading synced including
| backup copies of the material.
| bigbossman wrote:
| The problem with this (and Mendeley, Papers, Bibtex, etc.) is
| that each paper/thought is isolated. Roam Research
| (http://roamresearch.com/) is my new jam.
| pergadad wrote:
| What is Roam's financing/business model? So far the beta seems
| free but investing much time in a tool which then might
| significantly change is a risk...?
| luismmolina wrote:
| They are planning to charge $12-15 USD with an annual plan.
| mooneater wrote:
| How do you export? Seems like a wiki but proprietary?
| perchard wrote:
| Roam is awesome but this and other reference management
| software serves a different purpose (for me, at least). I use
| BibDesk (like Zotero and other examples mentioned here) in
| conjunction with a plaintext (markdown) Zettelkasten[0].
| BibDesk to save references (papers etc.) and copy formatted
| citations; which are then pasted into Zettels (c.f. a page in
| Roam).
|
| [0] https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-
| zettel...
| gpanders wrote:
| I do this exact same thing! If I write a new Zettel that
| references something I read in a book (for example), all I do
| is get the ISBN of the book (usually off of Amazon), use
| Zotero's auto-import feature, copy the reference and paste it
| into my note. The whole thing takes all of ~20 seconds, it's
| very efficient.
|
| I know Zotero has a lot of other features, but 99% of my
| workflow with it is what I described above.
| michael_fine wrote:
| Does roam support automatic importation of bibliographical info
| and export to bibtex? That's the main value of zotero for me.
| Also latex math embedding notes would be great
| asdff wrote:
| What exactly is roam? The website tells me nothing. Zotero has
| folders and tags for organizing your thoughts how you like.
| bloopernova wrote:
| See my comment reply to Chris2048 below your comment.
|
| It's a wiki like system that helps you to create a second
| brain of sorts. You write down what you do, and link between
| lots of different pages, such as "aws" to "ec2" to "vm" to
| "vmware" to "vmotion". Roam (and org-roam, an Emacs module
| that I use) shows you what links back to a page, which is
| incredibly helpful for remembering knowledge and how things
| fit together.
| bloopernova wrote:
| I'm gently easing myself into the Roam knowledgebase management
| style by using Emacs+org-mode+org-roam.
|
| It's definitely one of those topics where you could spend a
| huge amount of energy organizing but not much actually _doing_
| :)
|
| Regarding roamresearch.com: How do you find yourself
| writing/organizing pages? Daily journal with a log of what you
| did first, then linking out from there?
|
| (don't feel pressured to write a novel in response, I don't
| want to steal time from your day!)
| rollinDyno wrote:
| What I do is just annotate absolutely everything. I try not
| to think much about structure. What matters is that my
| thoughts are put down into text. Structure and organization
| comes later.
|
| Once your second brain is searchable, you can quickly find
| those keywords and the context thanks to Roam bidirectional
| links. This is one way to approach your notes, when you know
| what you're looking for.
|
| Another way to approach your notes is by browsing. You can
| create a page with the structure or outline that you come up
| with, and then fill them with links to blocks in other notes.
| In here, you can practice a step of progressive summarization
| and rephrase your notes.
| bloopernova wrote:
| Thank you, I appreciate you taking the time to respond! :)
| cycomanic wrote:
| The best application that I ever used for this was docear.
| Unfortunately it's not being developed anymore and some other
| things make it a bit painful to use. I'm still waiting for
| someone to integrate mindmaps with reference management in a
| better way.
| Chris2048 wrote:
| How does Roam differ from a wiki app like Zim/Tomboy?
| bloopernova wrote:
| Roam is way of using a wiki. i.e. you could quite easily set
| up a wiki to act in much the same way as Roam.
|
| The journal part of Roam, the page-per-day part, is very
| useful. You write down what you're doing each day, use tags
| and links to build up a second brain, so to speak.
|
| Let's say, today I'm working on kubernetes. I add a tag for
| k8s, which is a link to the k8s page, where I have all sorts
| of interesting links and notes dumped. When I'm on the k8s
| page, I also get a list of pages that link to the k8s page,
| which helps me to remember some other subject that might be
| relevant.
|
| It uses the Zettelkasten Method:
| https://zettelkasten.de/posts/overview/ and you can also get
| a lot of value from reading "How to Take Smart Notes" by
| Sonke Ahrens.
|
| The value also comes from it mirroring your thoughts and
| experiences, as I said, the second brain thing.
|
| (I'm terrible at explaining stuff, sorry :( I hope I didn't
| bore you to bits)
| getpolarized wrote:
| We're shipping a new version of Polar
| (https://getpolarized.io/) this weekend that is sort of closer
| to the roam/zettelkasten idea of managing notes.
|
| Here's a video explaining the new functionality:
|
| https://www.youtube.com/watch?v=6M6jNlairGc
|
| Basically all the documents you read can have tags. So you can
| manage all your documents via whatever tag you want.
|
| You can then read those documents in Polar directly and
| highlight parts of text that are interesting.
|
| These highlights, notes, comments, and flashcards that you
| create can also have tags.
|
| We call these annotations. We then have an annotation manager
| which you can manage by tag so you can pivot everything around
| the tags you're working with.
|
| This version is pushed to the web version of Polar now and the
| new desktop version will make it out this weekend.
|
| We're also working on a new Polar 2.0 which will support
| Android and tablets and have better pen support too so you can
| work directly in a tablet rather than a desktop/laptop.
|
| We're also working on a dark mode but first need to get 2.0 out
| the door.
| thatmathguy wrote:
| Would love to see an option to choose which pdf viewer Polar
| launches. Wouldn't mind losing out on some features (for lack
| of integration) as long as I can use my Evince.
| getpolarized wrote:
| You can sort of do this now but part of the power of Polar
| comes from using our own tools as they support new
| annotation features not present in other PDF readers.
| lbotos wrote:
| Consider adding a link to getpolarized.io on your youtube
| video descriptions. I opened your video, tabbed away, came
| back, watched it, got excited, and struggled to find your URL
| (which I happened to open in another tab from this comment
| :P)
|
| I'll be giving polarized a look this weekend and compare with
| zotero!
| michael_fine wrote:
| Does the new version handle citations/bibtex export? I really
| want to use polar but that's the main value of zotero for me
| atm.
| getpolarized wrote:
| We're getting there.. The backend supports it now. If you
| send me a list of your requirements (just create a github
| issue here https://github.com/burtonator/polar-
| bookshelf/issues) I will look at adding the functionality
| you need.
|
| We're adding support for DOI lookup and APIs like Arxiv so
| you could just add a DOI to polar and it will fetch the PDF
| and keep the metadata.
|
| Will also support export to bibtex too.
|
| Our big focus right now is shipping 2.0 so that we have a
| more modern platform that can scale us moving forward.
| michael_fine wrote:
| Great to hear! I'm actually a week away from finishing my
| undergrad thesis (ironically procrastinating on that
| now), so kinda stuck with Zotero for now. Once that's
| complete I'll take a good look at polar.
| fudged71 wrote:
| Would it be possible to export annotations into a
| markdown+wikilink syntax to import into Roam?
|
| I love the idea of Polar for document management, and Roam
| for knowledge management, so I'd love to find a way to use
| both
| getpolarized wrote:
| We're thinking of adding an generic sync functionality into
| Polar so that you could keep external connections to thinks
| like Anki, Evernote, Roam, etc.
|
| The biggest challenge is deletions though so I'm still
| trying to work out the ideal sync framework.
| rollinDyno wrote:
| Can Polar automaticlaly extract the metadata from a journal
| article?
|
| Also, while I can see tags being useful, I don't think it'll
| really be Zettelkasten-like until you can link from one
| annotation to another.
| getpolarized wrote:
| yes... I agree. I'm working on this too. The 2.0 UI will be
| all re-done in React, better mobile support, including
| transitions. So you will be able to deep link to other
| annotations by their ID.
|
| Also, going to work on the ability to link them together
| with a search and auto-complete system so that you can just
| start typing tags, or the body of the note, and then they
| can be linked.
| mrks_ wrote:
| Does anybody use this for non-academic purposes? I've been
| looking for something similar to use as a personal knowledge
| base, but zotero may be a bit much for that use case.
| djaque wrote:
| It ended up being the perfect solution for storing manuals and
| other random information for me.
|
| It's lightweight enough to not get in my way but still syncs
| everywhere and is searchable. There's even a third party app I
| can use on my phone if I need quick access to PDFs.
| boyband6666 wrote:
| As well as academic papers, I use it for storing copies (wiut
| hthe chrome plugin) of websites - things are not permanent
| these days and may reference sources I wouldn't want to lose!
|
| It's basically my personal library
| ohbleek wrote:
| Zotero is a game changer. Citations have become the easiest part
| of writing and the tagging feature is incredibly useful when
| doing a systematic review.
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