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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

#61

Post by ekphrasis »

decasia wrote: post #46
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…

Your information might be outdated -- In the latest version of Zotero, when you add a PDF to Zotero, it automatically retrieves the metadata via DOI lookup. (I don't think it would work with papers too old to have DOIs but haven't checked lately.)

The metadata retrieval pairs with a DOI or ISBN [1]. Articles without such handles might not work, nor will articles which are not OCR'ed (obviously) but this can be easily fixed with OCR scanning software.

The metadata retrieval process is a very handy feature, especially paired with Zotero's web browser plugin.

Zotero also keeps a repository of all the citation styles, which are curated and administered by the Zotero team and stored in a Github repo [2].

[1] https://www.zotero.org/blog/zotero-5-0-36/

|2] https://github.com/citation-style-language/styles

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

#62

Post by tonyg »

Sol- wrote: post #13
innocenat wrote: post #11

Zotero really need more advertisement. I prefer Zotero over Mendeley, but Mandaley seems to advertise much more to university.

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 system service.

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

#63

Post by zwaps »

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.

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

#64

Post by ekphrasis »

zwaps wrote: post #60
harry8 wrote: post #47

Earlier quoted context omitted.

Mendeley is an Elsevier product? Might make a few academics come to a differing conclusion given Elsevier's reputation is one they've well and truly earned...

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/1977/changing-the-defau...

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

#65

Post by bovine3dom »

zwaps wrote: post #60
harry8 wrote: post #47

Earlier quoted context omitted.

Mendeley is an Elsevier product? Might make a few academics come to a differing conclusion given Elsevier's reputation is one they've well and truly earned...

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.

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: the Mendeley mobile application makes selecting text a joy on a touchscreen with a kind of magnifying glass. I really wish it was built into Android system wide.

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

#66

Post by mblode »

For my university essays, I keep my research citations in Zotero and write in Markdown using Ulysses. Then when it is ready to submit, I'll use Raphael Kabo's technique [1] to export into Microsoft Word. It is a truly simple workflow to get perfect formating with little effort.

[1] http://raphaelkabo.com/blog/posts/markdown-to-word

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

#67

Post by tonyg »

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.

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, making it no longer accessible to the user (see downthread).

With Zotero, in principle you could hack together something using `bash` and `sqlite3` that batch-updated documents; you may not even need to look at the source code to the official app. It's ad-hoc munging like that that Mendeley has recently gone out of its way to prevent, stopping people from working effectively with their own data.

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

#68

Post by icelancer »

My company's R&D department uses Zotero a lot for our academic publishing. It's a little steep to get started as you build out the database but it's incredibly handy and well worth the time investment.

I've heard of other alternatives being better but shrug Zotero works well for us.

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

#69

Post by icelancer »

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…

>> I mean it is nice that Zotero has an import browser plugin (which, btw, Mendeley does as well), but once you have a substantial library of pdfs, it is just too time consuming to re-import it all again, type in names, years, journals etc. ugh..

It automatically added 90-95% of PDFs I imported, most directly from Sci-Hub with no editing from me.

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

#70

Post by tonyg »

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…

My experience of auto-import of metadata in Mendeley is that it gets about 80% of it right. Not good enough for publication: I still had to check over each record with a fine-toothed comb when I wanted to actually use an entry to cite something.

So far, Zotero's metadata lookup seems about the same quality.

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