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Zotero: Personal Research Assistant

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Re: Zotero: Personal Research Assistant

#121

Post by chispamed »

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 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

Re: Zotero: Personal Research Assistant

#122

Post by autocorr »

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.

Re: Zotero: Personal Research Assistant

#123

Post by tpudlik »

crazygringo wrote: post #94
xyzal wrote: post #66

Earlier quoted context omitted.

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

Does it have any kind of export functionality at all?

You can export to BiBTeX (.bib).

Re: Zotero: Personal Research Assistant

#124

Post by lbotos »

getpolarized wrote: post #68
bigbossman wrote: post #17

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.

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 hig…

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!

Re: Zotero: Personal Research Assistant

#126

Post by Woetoewoetoe »

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.

Re: Zotero: Personal Research Assistant

#127

Post by mncharity »

jmiserez wrote: post #72
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…

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

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?"?

Re: Zotero: Personal Research Assistant

#128

Post by stared »

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.

Re: Zotero: Personal Research Assistant

#129

Post by montalbano »

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…

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.

Re: Zotero: Personal Research Assistant

#130

Post by michael_fine »

getpolarized wrote: post #112
michael_fine wrote: post #82

Earlier quoted context omitted.

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.

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 bi…

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.
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