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Zotero: An open-source tool to help collect, organize, cite, and share research

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Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#81

Post by 131012 »

wycx wrote: post #75

5 years and 7464 references later Zotero has become an integral part of my workflow. The combination of Zotero and the custom renaming of Zotfile lets me store all my pdfs in Dropbox, but sync all database by Zotero such that I can add references at work and have them waiting for me on my PC at home. I abandoned Mendeley because it would not permit relative paths, and I have not looked back.

I loved zotfile for its feature which enable user to highlight/comment articles then import the text in notes related to article.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#82

Post by tonyg »

zwaps wrote: post #78
tonyg wrote: post #67

Earlier quoted context omitted.

I'm not sure what feature exactly you're missing, but are you aware of the "Rename file from parent metadata" option you get when right clicking on a PDF in the list? Perhaps that does what you need. If not, with Zotero you have a chance of getting a missing feature added. Not so with the closed-source Mendeley. Especially now they have started doing user-hostile lock-in stuff like gratuitously encrypting users' data…

Zotero can look up metadata if you add a PDF to your library Zotero can not update metadata for a PDF you already have in your library Hence, adding an existing library means you have to do it manually for each pdf This is bad design, because the functionality exists, but it's implemented in a way that makes everything complicated for no reason at all. Why disable the "lookup metadata" button for a pdf which is alrea…

I see! Yes, that's not great.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#83

Post by dstillman »

zwaps wrote: post #63
zwaps wrote: post #44

I use Mendeley instead of Zotero. I really wanted to like Zotero, since I hate Elseveir like the next guy, but Zotero didn't have any of the look-up features and ability to quickly import my papers (thousands). In Mendeley, I can just throw a physical folder into a folder and it'll tag and categorize the PDFs mostly correctly. I mean it is nice that Zotero has an import browser plugin (which, btw, Mendeley does as we…

yeah so I just reinstalled Zotero and imported my Mendeley library. It does that, and it can actually look up metadata from pdfs. But: It can NOT update already existing entries from such a lookup. You have to delete the pdf and re-import. Why? No reason. It's this sort of really bad usability decision that makes Zotero just not very good imo.

It's not a usability decision — it's just one feature that hasn't yet been implemented [1]. Updating metadata is more complicated than creating a new item, because you have to deal with the existing metadata somehow. (Mendeley just overwrites the existing item, often with incorrect data, which we don't consider acceptable.)

Disclosure: Zotero developer

[1] https://github.com/zotero/zotero/issues/1515

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#84

Post by Cenk »

anc84 wrote: post #76
Cenk wrote: post #30

Earlier quoted context omitted.

Citationsy works with Sci-Hub... just saying :) https://citationsy.com/blog/new-feature-citationsy-archives/

No export feature prominently advertised, this looks like another startup silo.

It can export CSL-JSON, BibTeX, Endnote, and RefWorks formats.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#85

Post by bovine3dom »

blattimwind wrote: post #80
bovine3dom wrote: post #65

Earlier quoted context omitted.

It's a bit of a pain, but you can store `~/.local/share/okular/docdata/` in version control or your favourite cloud storage provider, and then you'll get synchronised annotations. When I say a bit of a pain, I mean it - I switched to Mendeley with great sadness because its mobile application means I can read and annotate papers on my tablet and have it synchronised perfectly with my desktop. On a semi-related note: t…

> you can store `~/.local/share/okular/docdata/` in version control What kind of annotations are that? I think GP refers to document annotations, which are stored in the PDF file itself.

Annotations meaning notes, highlights, etc.

If they are stored in the file itself, that's news to me. Last time I used it, Okular didn't modify the actual PDF and considered that a feature.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#86

Post by michaelmior »

I had tried Zotero before but I stuck with Mendeley for a long time. I ended up using Zotero a couple years ago to share some references with my advisor and since then I've grown to love it. One of the nice things about it being based on Firefox is that there's a lot of extensions written for it (which IMO, are not well-advertised).

The API is also great and I've been using it to automatically sync PDFs of papers I want to read to my reMarkable tablet.

https://michael.mior.ca/blog/zotero-remarkable-sync/

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#87

Post by dstillman »

ekphrasis wrote: post #64
zwaps wrote: post #60

Earlier quoted context omitted.

I reinstalled Zotero just now, since it has a Mendeley importer now. What is the proper way to store PDFs that I annotate (say, using Okular in Linux) on Zotero with the ability to send them to other researchers and then update them? I don't mind paying money for cloud storage, but I gotta be able to work with the pdfs.

You can choose to set a custom PDF reader in the General tab of preferences --> Open PDF using --> custom [1]. Then you can annotate the file and save it. If Zotero creates a copy of the file when you save your annotations, you might need to use Show file by right clicking the article in Zotero and make changes to the file in Zotero's storage. In Linux, that'll be in ~/Zotero. [1] https://forums.zotero.org/discussion…

No need to use Show File. You can just open the PDF from Zotero, annotate, and save.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#88

Post by PaulRobinson »

tonyg wrote: post #62
Sol- wrote: post #13

Earlier quoted context omitted.

Even though I also like Zotero better because of its open nature, I prefer Mendeley in practice mostly because it has a decent Android client where you can just sync all your PDFs and read them on a tablet or something. Seemed a bit more involved to do the same with Zotero (where it seemed there were only minimal Android clients quickly hacked together). Mendeley also has 2GB storage, so that's nice for personal use…

I have found syncing the PDFs via Dropbox works fine. Zotero puts them in a Dropbox folder with a reasonable filename, and then the regular embedded Dropbox PDF reader does an OK job on my phone/tablet. It'd be nice to have the database synced, though. Funny how "synchronization of replicas of information", for all its centrality to modern internet-based life, isn't something that our operating systems provide as a s…

> Funny how "synchronization of replicas of information", for all its centrality to modern internet-based life, isn't something that our operating systems provide as a system service.

Just FYI on that front, macOS has iCloud, which does this. I put something on my Desktop, it appears on all my machines. I can access it from my phone, etc. etc. - it's basically a built-in Dropbox.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#90

Post by danielecook »

I am a big fan of paperpile:

https://paperpile.com

I've used Endnote, Mendeley, and Zotero before and found them all to have their own issues. Paperpile is not perfect but it shines in a few places and I really like it. The chrome plugin adds an 'add to paperpile' button to places like google scholar making it easy to add citations.

It also is designed for writing in Google Docs and makes it very easy and quick to add citations. For some, Google Docs may be a dealbreaker, but if you need to collaboratively write/edit a manuscript it's much better than the alternatives in my opinion (esp. because everyone can write/edit at the same time).

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