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[1] http://mackerron.com/zot2bib/
[2] https://groups.google.com/forum/#!topic/zotero-dev/a1IPUJ2m_...
My workflow is: 1. Come across paper pdf on the web. 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…
I'd rank the GUI experience this way:
Paperpile > Zotero >= Mendeley
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/
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.
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.
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 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.
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…
It's an open source project. Feel free to fork it and remove parts you dislike.
I for one am thankful for their warnings.
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…
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.