Zotero vs. Mendeley, Initial Thoughts

In my never-ending quest for ~~world-domination~~ a good PDF and bibliography manager I’ve been trying Zotero 1.5 beta and Mendeley 0.6.3 beta.

Both offer many of the same features. Tagging PDFs, extracting metadata, uploading PDFs to your account, etc.

I just never have been able to like Zotero, I’ve tried, alot, several times in fact. I just can’t get to like it for some reason. To me it seems like a separate program, not an add-on for Firefox, maybe that’s part of it for me. One of the biggest issues I have with the most recent version compared to Mendeley is the cramped UI. It just doesn’t work as well for me. Lastly, and this is a showstopper, when I installed it Web of Science quit working. Once I disabled it Web of Science came back for me, I get an Error 404. I didn’t look much further after that, if someone has a fix I’d be interested to hear it.

Mendeley is going the direction that I like and want. The interface is much easier for me to use mainly and it’s a standalone program with a web interface for when I need that sort of thing. That’s not to say Mendeley is perfect either. Since I’ve been using it the PDF metadata extraction can be erroneous and most frustratingly it crashes on me when trying to upload PDFs. I’ve about got all of them uploaded finally but it’s taken me several days of closing/reopening Mendeley to get it done. Just one niggle, Mendeley is free as in beer but not free as in speech. There is a feedback suggestion to publish Mendeleydesktop under the GPL here.

090320 16:10 – Updates –
Two items from Mendeley’s Feedback Forum.

It seems the problem I have with PDFs uploading is a Linux problem in general: http://feedback.mendeley.com/pages/general/suggestions/139511-error-unable-to-contact-mendeley-web

And

There is a suggestion in Mendeley’s feedback forum to work with Zotero, I like this idea.

It’s nice to see the developers addressing items in the feedback forum and moving forward. I know 0.6.3 is an improvement over 0.6.2 which I started using a few weeks ago.

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Published:: 20 March, 2009 / 09:15

Category:: Science, work

Tags:: Bibliography, bibliography management, citations, Mendeley, Zotero

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I’m a tinkerer. I tinker with computers, Jeeps, gardening, websites, blogs, whatever. Recently my outlet for my artistic tendencies has been photography. This blog focuses mainly on my photography but from time-to-time I throw in something of a how-to for Linux.

nortexoid 4.4.09 / 11am

Are you kidding? Mendeley (right now) is crap. The concept is nice but what they’ve implemented is unusable. The fact that it took you days to get all your pdfs uploaded is alone ridiculous. The same thing happened to me. And all for what? The awesome metadata retrieval that is completely inaccurate? No thanks, I’ll just add that info. myself, accurately and probably even faster (handtyping it!) than their sorry excuse for an algorithm does. I’ll stick to Zotero, CiteULike, and possibly Referencer (Linux). (Referencer does metadata retrieval too, but it never crashes and finishes the job within a lifetime.)

earlycj5 4.4.09 / 11am

Obviously I’m not kidding, I posted my thoughts here much as I allowed you to post yours.

Mendeley is making headway, I admitted it’s no perfect, but they’re working on it and for me it’s the program that most fits my needs. It is still beta so criticizing it for taking days to upload PDFs is silly. I know what I’m getting into when I try beta software. It’s not as mature as any of the other programs you mentioned.

nortexoid 6.5.09 / 5pm

C’mon, it crashes every 5 minutes trying to perform metadata retrieval! It’s one thing crash oncne in a while–that warrants saying “it’s not perfect, but…”–but when it crashes every 5 minutes (if you’re lucky) it receives NO praise.

Also, most beta software I use is usable, so it’s not quite the norm to expect this sort of horrid instability from beta software. They should call it pre-alpha or something.

earlycj5 6.5.09 / 5pm

Have you even tried the latest version?

I’ve started a draft about the latest version, but have been too busy with work to finish it.

Suffice to say the issues I had here haven’t reappeared.

So until you’re actually trying it and keeping up with the development of the software and not commenting on a version that’s an old version then I don’t see much point in continuing this discussion.

Jay I. Chok 10.29.09 / 1am

I’m starting to use Mendeley too. However, there is also another problem with using metadata extraction from the PDF itself – it can be dangerously inaccurate.

Right now, I maintained a zotero connection to Mendeley so if I had pdf documents that need to be checked, I’ll use zotero. The problem with Zotero is that if you upload hundreds of files to check with Google Scholar, you’ll get blocked. Also, Google Scholar is not the best verifier of references. Endnote is more accurate because it fetches the metadata directly from Thomson Scientific. Endnote X2 & X3 also allow you to find full text documents directly from the sources.

Just a final comment – Mendeley benefit tremendously from Zotero in the past, currently and in the future. I see that a lot of zotero users/developers are irritated about Mendeley. Perhaps it is because they felt that Mendeley only takes and do not give? Mendeley & Zotero should be allies, not enemies. The enemy is Endnote.

earlycj5 10.29.09 / 7am

I don’t agree or maybe it’s because I don’t understand, your final comment. I don’t see how Mendeley only takes and not gives, but I don’t use Zotero since I find it pretty useless to be frank.

As for metadata extraction, I just verify as I import. In fact, Mendeley tells you which references need to be checked. However if the DOI is present it seems work extremely well. I’m getting much less incorrect information with more recent versions anyway.

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