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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

#111

Post by smukherjee19 »

As a grad student, Zotero is a lifesaver! Thanks to the people developing it!

I use Google Drive for my pdf storage using some Zotfile acrobatics (awesome plugin btw) to manage my actual pdfs. I plan on switching to Zotero's cloud storage to support development as soon as I can.

That being said, I wish I had a nice workflow for reading papers on my iPad like I do on PC (Windows specifically, I know there are software for the Mac/iOS ecosystem but I don't have a Macbook so...): Open Zotero -> double-click on the paper -> Bam, the pdf opens in Acrobat where I can highlight and annotate, and save to pdf directly for future use.

The closest I got to this on iPad was to use the Zotfile plugin and use the Send to Tablet feature as described here [0], and opening and annotating the pdf on iPad.

Another interesting workflow seems to be using Obsidian to store the relationships between papers using annotations and highlights from them [1]. Another way to do this would be LiquidText but I paid 20+ USD separately for both the iPad and Windows Store versions, and it asks me to pay up again so I don't know what's up with them...

Still, I hope Zotero keeps being developed as it's the best, and perhaps the only open source research management software out there.

[0]: https://www.youtube.com/watch?v=e7novaC_O_Y

[1]: https://www.youtube.com/watch?v=_Fjhad-Z61o

EDIT: Added clarification of OS I am using.

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

#112

Post by hyperbovine »

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…

I thought the same thing until I discovered Paperpile. I highly recommend checking it out. https://paperpile.com

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

#113

Post by westcort »

Gatsky wrote: post #103
westcort wrote: post #40

I write a lot of academic papers and never use this kind of software. EndNote creates uneditable references and slows down Word, Zotero had some limitations after which they charge a monthly fee, and none of the reference libraries are easy to share with external clients. Most other medical/technical writers I know only use these tools as a “reference library.” It might be useful for someone writing a thesis, but alm…

Interested to hear more about this, so how do you create citations and bibliographies? How do you format the bibliographies according to each journal’s style? It is true that there is no good tool for editing references collaboratively. Previous attempts at this have resulted in some poor sod having to redo all the citations.

A RegEx-based parsing system in JavaScript helps with the reference formatting. EndNote makes references uneditable (unless you also have a copy of EndNote) and often cannot adjust to a particular journal's idiosyncrasies...but I can do that easily with home-built software.

Zotero may be great, and I cannot really make an assessment one way or the other. All I know is that hardly anyone in my industry uses it. It's really a nonstarter. Often, people need special permission to get access to open-source software and IT departments do not look kindly on installation of these tools.

Not to mention, I can't think of one piece of software or database I was using in 2003 that I can still access and use except for plain text files. This kind of software has no longevity. For these reasons, the academic publishing industry has not really standardized the process.

After a copy of RefMan broke, following the EndNote acquisition, I remember a time when I had to reverse engineer the database so I could still access the contents. It was a big tabular file and there was a much easier way to make it work with a simple browser-based tool and a few lines of code. I made it work and showed it to my boss, who summarily rejected the solution, even though it worked much better than the original (broken) software and broken database files for hundreds of prior projects. He emphasized that he wanted a paid solution. I still don't understand the logic. These are the kinds of nightmares that I associate with any kind of proprietary software solution. Often, in publishing, we need something that will work now and will still be accessible in twenty years. That's hard to do with free software.

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

#114

Post by solarkraft »

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 researchers or scientists do things, but so far what I mention above is the core of what I really need (mainly for personal research, but also the limited amount of scientific writing I've done).

I read about Zotero theoretically supporting these features, but when I last checked it out (about half a year ago) it looked antiquated, seemed to do a lot of things I don't care about and made the things I want to do so hard I was immediately disappointed and stopped bothering.

Are there any products (preferably FOSS, of course) that cover my use case? Is it possible with Zotero after all? I have tried Worldbrain Memex, but it also has such cumbersome UX it's not worth using.

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

#115

Post by solarkraft »

jjoonathan wrote: post #62
WayToDoor wrote: post #46

Earlier quoted context omitted.

> Mendeley went full on Evil Could you explain what happened with mendeley? I've been using it for a while, and didn't notice anything different really.

Hypothetically speaking: going to scihub, pirating an Elsevier paper, and then uploading proof that you had done so to an Elsevier cloud account doesn't strike me as the brightest of moves. Not in the sense that I think you are guaranteed to see consequences, or in the sense that I've actually heard about it actually going sideways, but to my intuition it does seem like the kind of thing that might attract one of tho…

Especially from that company.

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

#116

Post by westcort »

cycomanic wrote: post #81
westcort wrote: post #73

Earlier quoted context omitted.

Zipped folders of PDF files sent via e-mail.

Sharing zipped files of PDFs amongst people is quite possibly a copyright violation. Do you have distribution licenses for all the material you ar referencing?

I am curious as to how you share PDF files with others ensuring that you have distribution licenses for all of the files. Not even RightsLink from the Copyright Clearance Center automatically purchases those distribution licenses. What I do know is that other ways of sharing files do not have the same privileges of communication applied to e-mail in the law, so that is the reason why this is still the most commonly used strategy.

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

#117

Post by austinjp »

westcort wrote: post #84
cycomanic wrote: post #80

Earlier quoted context omitted.

You're getting down voted because you comment seems uninformed. AFAIK Zotero is available on every OS that Firefox runs on, for example. Also you talk professional publishing, what does that exactly mean? Zotero is a reference manager, so largely aimed at academic writing (because they tend to be the ones who cité and use references the most). I would be surprised if any other setting has more stakeholders, scientifi…

Let’s say you are working on a paper with 6 coauthors for a major medical journal, hypothetically. Dr. So and so in Russia, another in Japan, a third in California, and a few others. Would you mind reviewing this draft? Oh, yeah, by the way, you need to install Zotero before you can edit the references. How do you think that is going to go? How about dealing with a graphic designer in Hungary who can’t copy the text…

For what it's worth, I've seen the same sort of interoperability issues with all similar software. Author A wants "the latest copy of the Endnote file" but nobody's using Endnote; Author B insists on emailing PDFs as attachments and uses their email as their personal literature database; Author C has set up a Dropbox full of PDFs but nobody uses it; Author D has created a shared Google spreadsheet with links to each paper but it's always out of date; etc etc etc.

These aren't issues with any one piece of software, they're issues with coordination, as are the examples you mention.

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

#118

Post by solarkraft »

dfraser992 wrote: post #56
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…

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.

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

#119

Post by maweki »

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.…

I'd like to additionally suggest syncthing to sync the PDF folder and, as you suggested, use the free account only for the metadata.

Works like a charm and I have all my literature synced up.

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

#120

Post by kuhewa »

medimikka wrote: post #58
turboaspie wrote: post #51

Earlier quoted context omitted.

>Zotero can do anything EndNote can do, is Open Source, and with that won't drive your PI up the wall with yet another expense. My university offers EndNote (plus Web of Science and the Clarivate stack) for free for students and many of them don't use it - they'd rather manually manage the bibliography in their Word documents. The university even ran tutorials to show them how to set it up, add citations, and export…

Did you use EN9 or EN20? I found EndNote to be usable, just not something I'd pay $130 (student/academic version) for.

It took me until the update to 20 to realise it, but it was Endnote X9 i.e. 19, not 9
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