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Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

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Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#151

Post by jsilence »

austinjp wrote: post #110

Just another user here, sharing some tips: Zotfile allows automatic renaming of attachments, which includes moving the PDF file to a different folder. This means my zotero account still has plenty of free storage, while the space-consuming PDFs are stored in my university's effectively limitless cloud drive. I use Recoll to fuzzy-search the text of the PDFs, or just pdf2text piped through grep for simpler searching.…

"Zotfile allows automatic renaming of attachments, which includes moving the PDF file to a different folder. This means my zotero account still has plenty of free storage, while the space-consuming PDFs are stored in my university's effectively limitless cloud drive."

Wow, did not know that. Have to test this! Thank you!

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#152

Post by jsilence »

solarkraft wrote: post #114

I just want something where I can import stuff (most importantly web pages, pdfs, epubs), read (on my e-reader), mark things/take notes, search and turn highlights into citations. The desktop version of Citavi and Zotero seem extremely overloaded. The web version of Citavi is the closest to this I've seen (it has a mode for highlighting), but it still absolutely sucks. Maybe I don't get the hang of how real researche…

As a counterpoint to your sentiment: I am really glad Zotero devs are not spending any time on polishing the UX. I loathe modern user interfaces where a lot of functionality is hidden just for the looks.

Zotero does cover your use case very well and I don't actually see your criticism or UX concerns.

For easy importing of books and papers use the magic wand icon in the tool bar. This allows you to import metadata via ISBN and DOI. Use the FF plugin for importing web pages.

Tags allow you to cluster entries together.

On the right side it is possible to connect items that have a direct connection.

Double click on Pdfs to open them in a Pdf reader that can highlight and annotate. Save the file and use the Zotfile plugin to extract the annotation into notes.

Zotfile and Zutilo are recommended plugins.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#153

Post by dstillman »

japanuspus wrote: post #146
medimikka wrote: post #35

Zotero is, if you're not in the market for a closed source silo like EndNote, the only game left in town. Mendeley went full on Evil, and Papers for Mac is Mac only, closed source, and missing dozens of functionalities that are absolutely a must have in academic writing and research. An absolute must have is BetterBibTex ( https://retorque.re/zotero-better-bibtex/ ), which adds better Citekey management and, my perso…

If the town is "online reference managers," you are probably right, but I would argue that reference managers are one of those areas where you really want something offline: - Offline ensures that you do not suffer an externally caused downtime just before a deadline - Offline ensures that you have a path for keeping your database throughout your research career, and to do system updates when _you_ want to. - Offline…

Just to be clear, Zotero is primarily a local program that saves all data and files to your computer. You don't need an account to use it. There's optional syncing and a web library so you can use it on multiple devices and collaborate with others, and there's a browser extension (which JabRef uses as the basis for their extension) that integrates it deeply with the browser, but in no way is it an "online reference manager". We strongly agree with all the reasons you give, which is exactly why we designed Zotero the way we did.

(Disclosure: Zotero dev)

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#154

Post by shaicoleman »

Ostrogodsky wrote: post #97

I love and I use exclusively Linux but sometimes I despair: > How do I install Zotero? Mac Open the .dmg you downloaded and drag Zotero to the Applications folder. You can then run Zotero from Spotlight, Launchpad, or the Applications folder and add it to your Dock like any other program. After installing Zotero, you can eject and delete the .dmg file. Windows Run the setup program you downloaded. Linux Download the…

There's a flatpak version available:

https://flathub.org/apps/details/org.zotero.Zotero

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#155

Post by jrichardshaw »

I've tried to use Zotero over the years, and I always stumble with it because it didn't have a good handling of arXiv id's. The arXiv is one of the primary way of finding papers in my field (cosmology), and I really want to support ingestion via them, looking up actual paper details from them (while retaining the arXiv id), and including them in bibtex exports. I check back from time to time, but I don't think that's massively improved, but I would be very happy if anyone else knows otherwise.

Although it's gotten a little maligned here, I've actually switched to Readcube Papers recently, it supports everything I list above, and has been pretty good for everything else. It's a closed source and subscription which isn't ideal, but in the end I'm willing to pay for something that supports my workflow. I do worry a little about getting locked in, but ultimately, provided I'm willing to ditch any annotations, I think I can just export everything as bibtex and import to something else.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#156

Post by diarrhea »

dstillman wrote: post #153
japanuspus wrote: post #146

Earlier quoted context omitted.

If the town is "online reference managers," you are probably right, but I would argue that reference managers are one of those areas where you really want something offline: - Offline ensures that you do not suffer an externally caused downtime just before a deadline - Offline ensures that you have a path for keeping your database throughout your research career, and to do system updates when _you_ want to. - Offline…

Just to be clear, Zotero is primarily a local program that saves all data and files to your computer. You don't need an account to use it. There's optional syncing and a web library so you can use it on multiple devices and collaborate with others, and there's a browser extension (which JabRef uses as the basis for their extension) that integrates it deeply with the browser, but in no way is it an "online reference m…

I use Zotero and sync the attachments to my Nextcloud instance via WebDAV. The database is synced to the Zotero servers, because that's the only option. With a bit of care on initial setup for new machines, it works wonderfully. The real value are the PDFs, some of which are of course really hard to get by. And those are "local" in the sense of "local server", yet available to all clients.

There was a forum entry that self-hosting the database is a topic being worked on. That's my number one gripe with Zotero, it just seems weird: if using multiple clients, users have to sync to the Zotero servers, yet the storage space for attachments there is minimal (which is okay; Zotero pricing looks reasonable but of course, own storage via e.g. Nextclodu is much, much cheaper). This basically forces a hybrid solution, with bring-your-own-storage. If all of Zotero's data could be self-hosted, now that would be a streamlined, great experience.

Then again, I am anal about my entries' metadata and often correct faulty data found online. Syncing that to Zotero servers is kind of like giving back? I always thought that data might help improve Zotero's own auto-fill functionalities, which I'd like helping with.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#157

Post by dstillman »

jrichardshaw wrote: post #155

I've tried to use Zotero over the years, and I always stumble with it because it didn't have a good handling of arXiv id's. The arXiv is one of the primary way of finding papers in my field (cosmology), and I really want to support ingestion via them, looking up actual paper details from them (while retaining the arXiv id), and including them in bibtex exports. I check back from time to time, but I don't think that's…

Zotero has supported adding items via arXiv ID since 2018, and saving from arXiv.org since forever. There's not currently a dedicated field for arXiv IDs, but they're added to the Extra field and included in exports (and accessible however you want via Better BibTeX export).

(Disclosure: Zotero dev)

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#158

Post by dfraser992 »

solarkraft wrote: post #118
dfraser992 wrote: post #56

Earlier quoted context omitted.

I forget why I didn't like Zotero - I am using iLibrarian [0]. It is positioned as a SaaS, but the source is available and you can host it yourself. But I can't speak to how it compares to other software as I am not continually using it. It seems I just like collecting scientific papers rather than actually reading them.... Maybe if I live to 150 will I manage to read them all. [0] https://i-librarian.net/ And I whol…

Oh damn. It looks extremely close to what I want (It's responsive and the PDF UI might even work on my e-reader), but it doesn't seem to support importing web pages?!?!?!?!?!?!?!?!?!?!?!?!?!?! What a massive and disappointing oversight. Otherwise I could've seen it becoming my new research manager.

I print the webpage to a PDF and store it that way, then fix up the metadata as I see fit. And that is a good feature - make a request on the Github repo and see if the lead developer responds.

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#159

Post by dstillman »

diarrhea wrote: post #156
dstillman wrote: post #153

Earlier quoted context omitted.

Just to be clear, Zotero is primarily a local program that saves all data and files to your computer. You don't need an account to use it. There's optional syncing and a web library so you can use it on multiple devices and collaborate with others, and there's a browser extension (which JabRef uses as the basis for their extension) that integrates it deeply with the browser, but in no way is it an "online reference m…

I use Zotero and sync the attachments to my Nextcloud instance via WebDAV. The database is synced to the Zotero servers, because that's the only option. With a bit of care on initial setup for new machines, it works wonderfully. The real value are the PDFs, some of which are of course really hard to get by. And those are "local" in the sense of "local server", yet available to all clients. There was a forum entry tha…

See my comments on [1] for why we don't support self-hosting. Short version: it would pretty much just be an entirely different project.

> Syncing that to Zotero servers is kind of like giving back? I always thought that data might help improve Zotero's own auto-fill functionalities, which I'd like helping with.

No, we don't expose your data to anyone else. (And tools that try to do that usually just end up filling people's libraries with junk data.)

You should sync Zotero if you want to 1) access your library on other devices, 2) collaborate with others, and/or 3) have a real-time backup of your Zotero data.

[1] https://github.com/zotero/dataserver/issues/105

Re: Zotero: Free, easy-to-use tool to collect, organize, cite, and share research

#160

Post by thenoblesunfish »

Once I bailed on Mendeley, I considered other options, but found that most of my needs were satisfied by simply:

- a canonical naming scheme for references in my single BibTeX file - a directory of PDFs using those names

I have some for-fun little vim macros to e.g. use “open” (OS X) to open a PDF corresponding to a canonical reference name.

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