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.
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?
First thought for easy digitization of hand written notes is an iPad with pencil by your workstation. A BKM for integrating that into your Zotero workflow isn’t obvious though.
That's the article I first read about it in. It's great, it really has the main ideas and how to implement it in a paper card system. The "How to Write Smart Notes" book is also great and a short read. It can get a little too pop-pyschology-esque in some parts for me (I just skimmed over those parts), but it is probably the most thorough writeup on Luhmann's system in English.
I'm currently contemplating how to use it as functionally as possible (categorise articles by subject? By hypothesis? Both?), so would love to chat about it if you'd like
Just wrote a short summary of my method to a friend. Might not be terribly readable for people who haven't used Roam, so take it for what it's worth. Hope it's for some use :-)
What I do is an interaction between the following:
So I might read an article, then tag the article/figures with the relevant tags. If it's for a specific project, I keep a list of tags on a separate page. This ensure that I use the tags consistently, so that I can find all the relevant articles later.
I purposefully keep the tags general, like "psychiatric conditions" rather than "depression, mania, schizophrenia" etc. When I reach the hypotheses page, this means that I can form relatively general hypotheses, and then nest them into gradually more specific hypothesis that are specifically supported by the articles.
Then, I use those hypotheses to form new predictions. These predictions turn into new research questions, which I either explore via the literature or doing my own experiments.
An example of this might be:
"Wood 2018" <->
#Procedural Memory #Habits <->
Habits are part of procedural memory [[H]] <->
Habits are part of procedural memory [[H]] & Procedural memory is stored in the basal ganglia [[H]] <->
Damage to the basal ganglia disrupts habits [[H]] <->
Seger 2011
This affords me a lot of flexibility in total processing time; I don't spend a lot of time forming hypotheses that aren't interesting/necessary for me, I can quickly tag a lot of sources, and I can quickly collate those sources on a specific topic when necessary.
You might say that the first half of the workflow is "induction", the second half "deduction and confirmation".
I would love it if you had any questions or comments, but just writing this up has been useful for me as well.
Do you by any chance also have some experience with taking general (think college) notes in this way? I'm a STEM student and having a hard time with organising knowledge to be both useful on exams (i.e. containing hard facts, proofs) and _after_ them (i.e. containing intuition, connections). I'd be happy to chat about this as well.
You can shoot me an email on "mr [dot] sh4rpeye" at gmail.
Yes that was kind of vague! Zotero has an interface for taking simple text notes[1] that can either be stand-alone or attached to bibliographic entries like books or articles. In my Zotero library I have folders for different media like journal articles, conference proceedings, books, proposals, etc but don't organize them by subject. So for my literature notes I just attach them directly to the bibliographic entry. I usually try to keep these short and just write down interesting ideas or thoughts rather than summarizing the content (if they're short I'm more likely to actually write them!). As a separate folder in my Zotero library I just have one big pile of stand alone notes that I like to call my "memex" (analogous to Luhmann's Zettelkasten). By flat folder, I just meant that I don't attempt to organize the notes into a subject hierarchy (e.g., "galaxies / spiral / high-redshift"). The stand-alone notes can then be linked to each other with the "related items" feature (to other notes and relevant journal articles mostly). Luhmann's main insight I think was in not trying to impose a universal hierarchy on his writings but to organically grow a system of inter-connected thoughts through these item-to-item links. The mental act of identifying the most important links helps cultivate original thoughts. Needing to manually walk the notes puts you in a sort of conversation with yourself and means you engage with your past writings and ideas. Zotero isn't perfect for this, but the system is very simple, and can be done with paper cards, a single text file, a wiki, or special purpose software. But since my most frequent work flow is "thoughts related to journal articles", Zotero's bibliographic functions and the fact that that's where the PDF files are, make it much simpler to use for me than a stand alone tool.
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.
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.
Is, for now. The parts of FF that Zotero relied on are being phased out (listed on the Mozilla docs site as "Archive of obsolete content"), so a transition to Electron is planned, and as part of that transition plan, parts are already being rewritten from XUL into React/HTML.
I like the Firefox bookmarks manager a lot, especially the tags you can apply to a bookmark then search on.
If I get good enough with Lisp, I want to write an importer that takes all the tags from my bookmarks sqlite db, write them into org-mode files with each tagged bookmark listed in the relevant file.
I think citationsy addresses a different public -- it looks to be more like ZoteroBib (zbib.org) or the web-client of Zotero than Zotero Desktop. Citationsy is going to be convenient for one-offs, but it's very common to shop around a paper until it is accepted somewhere, or submit a follow-up paper that builds on an earlier one, and each outlet may have different citation style requirements. Tools like Zotero (and Mendeley) make that fairly easy because you can just switch the style and re-render the document, and you're (ususally) done. With citationsy, as far as I can tell, you'd need to revisit every reference in the paper to adjust it to the new style. And while it seems to have fallen out of favor, I don't think citationsy can do ibid-style referencing.
I'm not sure I can buy into citationsy. From its website, there's too much contradictory marketing hype:
> We don’t have to promise to keep your data safe — because we don’t collect it in the first place... Citationsy lives in the cloud and is accessible from anywhere... Your data is saved in the cloud and backed up every 10 minutes
> Nothing to install, update, or patch... Use our iPhone and Android apps to cite books on the go with our barcode scanner and add the Chrome or Firefox extensions to cite websites in 2 clicks.
Perhaps I missed the use case where you retain your data, or there's a version you can self host?
The first sentence should read “personal data”, but you’re right, the copy is not great. To be fair though, you compiled bits of sentences from completely different sections to make it look more contradictory than it is.
To be clear, Citationsy has no tracking and collects as little personal data as possible.
When you cite something we keep your citation data on our servers, of course. You can download all your citation data at any time in various open formats (BibTeX, CSL-JSON, etc).
Yes, but they’re about different things - one is about personal data and our privacy policy, and the other is about how there is nothing to install, update, or patch when using Citationsy, and all your references are kept safely in the cloud. Our privacy policy is very clear on what data we keep (in fact we link to it from one of the sentences OP omitted above - https://citationsy.com/privacy ). The sections are entirely consistent, unless you take a couple random sentences and disingenuously mush them together.
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
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.
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.
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.
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.
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.
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.
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.
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.
You do realize that (unless something changed recently) all your metadata is still on their servers? Last time I checked, a Docker image of the sync server was in the works though.
...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!
This conversation is now days old, and people have moved on, but here's one quick belated thought. No reply needed, just fyi, fwiw. I was at an embassy party years ago, and apparently a friendly European embassy, in a US city, had a couple of people keeping track of local research, and doing heads-up for their national industry and academia. That's just one embassy, in one city. I suggest Zotero has very different threat profiles across different fields and research topics. And for some, the possibility of state actors should be included. Which suggests a need for users to easy notice and adjust their exposure profiles. And is a reminder that the user data Zotero servers are least likely to compromise, is data that's never seen at all. Fwiw. Thanks again for your work.
Love Zotero. I'd love to install it on my own server instance, although, I think by renting the Zotero storage space now, I'm helping support you and the whole Zotero project.
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.
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.
Thanks for your thoughtful replies. I see one clear disagreement, and speculate about a more-root divergence.
> configurable in one place in the software just isn't reasonable [...] auto-sync doesn't have anything to do with translator update checks
Microsoft has in one place (something very vaguely like) toggles to control the uploading of web history, hand writing, voice commands, and more. Different features of different apps. With explanations of the functionality lost if the user doesn't opt-in to each. One place, for privacy preferences.
The Zotero privacy documentation page similarly gathers in one place, recipes for opting-out of network-based features, with descriptions of use.
Software preferences having a privacy section is a thing. Firefox, chromium, etc.
I'm unclear on why it isn't reasonable for Zotero software to have similar.
> we consider privacy in all our decisions and believe we've made the right calls [...] If you disagree with a specific decision, that's fine — come to the forums and we can discuss
I suggest there's currently a shift in privacy best practices, from one-size-fits-all "make the right calls", to having user preferences for privacy.
So that's the sort-of clear disagreement.
But part of it may be a deeper difference in perspectives...
perhaps call it network minimalism.
When using Zotero, I'd spend more time grovelling over previously collected papers, than collecting new ones. A task that could be done, without loss of functionality, with the net disconnected. My expectation then is, that this local tool, working with local data, will not then start using the net merely because it becomes available. Or rather, that I can easily dissuade such behavior.
Now perhaps that expectation is becoming "old fashioned", as we switch from desktop, to phone apps with only lightly bridled communication lives of their own.
Which might be an underlying issue. Zotero might be thought of as a phone app which just happens to run on desktop-local data. Or it might be thought of as a traditionally desktop application. Design decisions appropriate to the former, might feel a bit odd in the latter. "Local tool" might mean different things.
> I can't recall a single complaint about our approach
In this thread, there was someone suggesting my short paraphrasing of the linked docs was getting it totally wrong. I'm not sure how widely your users are even aware of the approach. It seems users generally aren't. Which, tying things back around, is one of the motivations for having clearly explained privacy preference options.
Thanks for an interesting conversation. Just in case you haven't seen it, the subthread with jmiserez might also be of interest.
> Software preferences having a privacy section is a thing. Firefox, chromium, etc.
Yes, and Firefox's Privacy & Security section doesn't cover Firefox Sync, the default search engine, search bar suggestions, the new tab pane, the default homepage, or app update checks. Those all make network requests to various services, and they're all controlled in their own sections in the preferences where they make more sense. And you can't turn off loading a website when you enter a URL.
Grouping a few more prefs together in Zotero might make sense, but in a modern, web-connected tool, there's just a lot of functionality where the network connectivity is implicit. The main difference in Zotero is that we document it all and tell you how to turn it off.
Specifically switched over to Zotero because of the non-profit status. The only privacy feature request I'd make is to allow some kind of self-hosted sync, i.e. a deployable TLS sync server + preferences entry to specify a sync server ip/port. I imagine it would take load off you guys for syncing, and people would end up hosting sync servers for small groups on university networks.
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.
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?"?
>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.
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.
I think dstillman put it best, the features that make Zotero actually useful need to connect to the internet, like fetching metadata. You wouldn't want to enter everything by hand (but you can).
I think your expectation is reasonable (a local tool will be offline when using only local resources), and it's definitely possible with Zotero (disable the automatic translator/style updates) but just not the default setting.
On a technical level, I don't think there is a huge difference between polling and maintaining a persistent connection, if the polling interval is short or the keepalives are long. The real question that I'd find interesting is why the translator/style updates must be "instant". For my use, once a day or once every few hours would probably be more than sufficient.
> The real question that I'd find interesting is why the translator/style updates must be "instant". For my use, once a day or once every few hours would probably be more than sufficient.
Before Zotero had push-based auto-sync, translator/style updates were indeed once a day, but that meant that, if a high-profile site changed and we pushed out an updated translator, we'd continue to get reports of the site being broken for 24 hours. We could say to update translators manually, but that would only help the people who made it to the forums.
When we added WebSocket support for syncing, we decided to send translator/style update notifications over the same connection. For anyone using auto-sync anyway (many/most users), there's no difference. If you don't use syncing/auto-sync, it's more debatable, but it's a choice between trying not to expose IP addresses that are likely already making at least some other anonymous requests (app updates, retraction checks, OA PDF checks) and decreasing the amount of breakage that users encounter after we've already fixed something.
Nod. One way to address conflicting desires for both opt-in and defaults, is having an onboarding step "want to use net for features... can customize under Preferences/Privacy... [ok]". Informed and consent is somewhat spread in time, and between the step and preferences, but... it seems current best practice.
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.
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.
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.
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!
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.
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.
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.
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.
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.
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.
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).
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.
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!)
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.
I'm actually trying to free myself from the habit of organizing/structuring/planning. It gets in the way. Still obviously experimenting.
I'll usually just start putting things into Daily Notes, but if a connected set of notes gets too long, I'll make a separate page and add a [[]] link in the Daily Note.
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...?
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.
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
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 Sönke 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)
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.
Seems to me this is like tagging, but instead of making the tags at the end of your thought, you're annotating words within your writing, which become the tags. I grant you that it is more intuitive to do it this way.
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.
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.
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.
You lose your folder organization (a.o.) that way. There used to be a direct import of the database into Zotero (much like Mendeley can do direct import of Zotero DBs) but that has become impossible since Mendeley have encrypted their database, for which they hand-wave to an unspecified GDPR article that apparently forces their hand, but not Zotero, Excel, or a million other apps that you use to process your own data. Plenty of people have asked Mendeley on Twitter to clarify exactly what article would compel this over the past two years, with not a single public response by Mendeley.
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.
I use zotero and store the pdf files (renamed and organized with ZotFile) on OneDrive. I can read papers and make highlights/notes to pdfs and they will sync to all of my devices. These notes can be extracted and made searchable within Zotero by Zotfile.
At first I preferred the way that Mendeley did this with its built in pdf reader, but now I'm happy Zotero delegates to the pdf software of your choice.
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)
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.
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).
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.
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.
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!
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.
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.
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.)
This. The paper I want to cite, I actually make an effort to go to its author's website and grab bib from there. That's the only definitive source of how the author wants to be cited. Grabbing bib from automated tools has created bib hell that we rely upon Google Scholar to clean up via fuzzy matching which screws up things quite often.
That works if it's the author itself, and the author has at least a passing familiarity with BibTeX. Much of the bibtex that you can download from journal cites is itself pretty botched up.
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.
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?
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.
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 :-)
Sync your metadata with Zotero but the files in the cloud - you just need to make sure your settings are compatible between machines (storage locations etc).
That's what I do, but it took a while to get there.
Since I would say 80% of people have some level of cloud storage now (University, employer, personal), there should be a simple setting to pick one, and the location. Make it easy for people and win users!
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.
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?
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.
One good habit is to never import using the browser plugins until the page is fully loaded. Otherwise, papers often get imported as web pages with no PDF attachments.
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.
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.
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.
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)
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.
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.
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]. :(
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.
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:
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.
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.
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.
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!
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?
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.
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.)
I'd be interested to learn more about Zotero's history and whole space. Do you mind if I reach out to you with more questions? Email's on my profile :)
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.
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.
Does anyone know of a comparable tool for legal research (or plugin(s) that add this functionality to Zotero)? A good friend is in law school right now and has really been wanting a good citation manager, but when I pointed him to Zotero it ended up being lacking due to the absence of a standardized reference number and citation info that scientific papers have.
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.
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'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.
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.
I'm using diigo for the same purpose. It seems to have similar features and more, especially easy tagging instead of having to deal with folders. Diigo also allows annotation, offline copies, search within text, export whole collection etc.
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?
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.
No way I could have written so many papers in so little time in my undergrad Poli Sci major. (2005-2009)College without this would have been a bigger nightmare.
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.
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.
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.
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.
* 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.