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Zotero: Personal Research Assistant

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Re: Zotero: Personal Research Assistant

#201

Post by retorquere »

dotdi wrote: post #11

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 onl…

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.

Re: Zotero: Personal Research Assistant

#202

Post by retorquere »

jmiserez wrote: post #77
sidpatil wrote: post #58

Earlier quoted context omitted.

> 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.

Zotero is/was a XUL application, and the whole application used to (also) be a Firefox plugin. So the similarities are not unexpected.

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.

Re: Zotero: Personal Research Assistant

#203

Post by retorquere »

tpudlik wrote: post #123
crazygringo wrote: post #94

Earlier quoted context omitted.

Does it have any kind of export functionality at all?

You can export to BiBTeX (.bib).

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.

Re: Zotero: Personal Research Assistant

#204

Post by retorquere »

sytelus wrote: post #184
memming wrote: post #84

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.

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.

Re: Zotero: Personal Research Assistant

#205

Post by retorquere »

ajot wrote: post #56
ansible wrote: post #19

Earlier quoted context omitted.

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?

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.

And most of such styles are so-called "substyles" -- if the master style they derive of changes, so do they.

Re: Zotero: Personal Research Assistant

#206

Post by inakarmacoma »

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…

DynaList might complement your approach, for the earlier unstructured collection and task brainstorming

Re: Zotero: Personal Research Assistant

#207

Post by tlavoie »

souterrain wrote: post #150
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…

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/…

For what it's worth, Pinboard also has an API that you can use to manage your data, including making backups.

I use it for exactly that, especially since he's quite upfront (and funny) about how hooped everyone could be if he's ever hit by a bus.

Re: Zotero: Personal Research Assistant

#208

Post by Eugeleo »

ryqiem wrote: post #199
ryqiem wrote: post #196

Earlier quoted context omitted.

I think you might find Roam Research ( http://roamresearch.com/ ) to be useful for this! 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: Article Tags Hypotheses Synthesis Prediction Research 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…

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.

Re: Zotero: Personal Research Assistant

#210

Post by mncharity »

dstillman wrote: post #70
mncharity wrote: post #57

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/suppor…

(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…

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.
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