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Zotero: Personal Research Assistant

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Re: Zotero: Personal Research Assistant

#131

Post by dstillman »

mncharity wrote: post #117
dstillman wrote: post #70

Earlier quoted context omitted.

(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…

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…

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.

Re: Zotero: Personal Research Assistant

#132

Post by boyband6666 »

MengerSponge wrote: post #102
131012 wrote: post #34

Earlier quoted context omitted.

I highly recommend the zotfile plugin! In itself, this plugin made zotero more interesting than the competition.

Zotfile + Better Bibtex is the ticket for me

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!

Re: Zotero: Personal Research Assistant

#133

Post by boyband6666 »

mrks_ wrote: post #73

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.

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

Re: Zotero: Personal Research Assistant

#135

Post by bloopernova »

rollinDyno wrote: post #95
bloopernova wrote: post #27

Earlier quoted context omitted.

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 nov…

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 you…

Thank you, I appreciate you taking the time to respond! :)

Re: Zotero: Personal Research Assistant

#136

Post by [deleted] »

cproctor wrote: post #106
Freak_NL wrote: post #40

Earlier quoted context omitted.

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…

Pairs well with a USB barcode scanner.

[deleted]

Re: Zotero: Personal Research Assistant

#137

Post by jMyles »

autocorr wrote: post #122

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 met…

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...

Re: Zotero: Personal Research Assistant

#138

Post by boyband6666 »

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 :-)

Re: Zotero: Personal Research Assistant

#139

Post by dstillman »

stared wrote: post #128

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…

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.)

Re: Zotero: Personal Research Assistant

#140

Post by tmalsburg2 »

abdullahkhalids wrote: post #78
tmalsburg2 wrote: post #63

Earlier quoted context omitted.

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…

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.
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