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Zotero: Personal Research Assistant

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Re: Zotero: Personal Research Assistant

#171

Post by cmroanirgo »

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'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?

Re: Zotero: Personal Research Assistant

#172

Post by luroc »

jMyles wrote: post #137
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...

The book 'how to write smart notes' is a great writeup un that topic.

This post is quite good aswell: https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettel...

Re: Zotero: Personal Research Assistant

#173

Post by radus »

bovine3dom wrote: post #22
tobias2014 wrote: post #8

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/

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.

Re: Zotero: Personal Research Assistant

#174

Post by dstillman »

mncharity wrote: post #157
dstillman wrote: post #131

Earlier quoted context omitted.

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…

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 di…

> 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.

Re: Zotero: Personal Research Assistant

#175

Post by radus »

boyband6666 wrote: post #138

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 y…

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).

Re: Zotero: Personal Research Assistant

#177

Post by autocorr »

luroc wrote: post #172
jMyles wrote: post #137

Earlier quoted context omitted.

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...

The book 'how to write smart notes' is a great writeup un that topic. This post is quite good aswell: https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettel...

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.

Re: Zotero: Personal Research Assistant

#179

Post by autocorr »

elcomet wrote: post #148
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 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 ?

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.

[1] https://www.zotero.org/support/notes

Re: Zotero: Personal Research Assistant

#180

Post by fudged71 »

getpolarized wrote: post #111
fudged71 wrote: post #89

Earlier quoted context omitted.

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

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.

That would be so great!! I think a plain export would be useful to someone at somepoint though, in addition to sync :)
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