Zotero

[urgnom]

How many of you are using Zotero and what do you think about it? I think it is superb, much more friendly to work with than Endnote on Windows/OS X. Even integrates with OOo :-)

[jraab22]

Its a brilliant piece of work, I love it. My biggest complaint is some sites seem to go in and out of support. The PLOS sites most specifically, I doubt this is zotero's fault , and an easy workaround is to snag the citation from pubmed, but its not quite a flawless system yet.

[akniss]

Zotero is okay, but I'm not a big fan of having my bibliographic software being a browser plugin. I personally use Bibus. Its worked great for a PhD dissertation and several peer-reviewed papers.

[machoo02]

+1 for Bibus

[amar]

Had never heard of it but it looks like there is limmited-no LaTeX support :( I have generally used google notes for browsing and recording sites/papers with useful info before adding them to kbibtex at a later date

[urgnom]

Well, it doesn't support texing directly, but you can export the library as a bibtex file, which works fine for me :-). I suppose the Zotero people will do something about this one day....

[xadder]

I just discovered the joys of jabref, and since I am almost 100% LaTeX this suits me perfectly. For me one of the big advantages of jabref is that there is no fancy database, or need for a browser even - eveything is stored in my simple ascii (or UTF-8) bibtex file. jabref is also great for importing different types of citations, great for searching, and has links to my pdfs.

Nothing against Zotero, but for LaTeX users I can recommend checking out jabref at least.

[parktownprawn]

I initially liked zotero buy it seems to get quite sluggish and unwieldy if you have a large (ie. hundreds) database of references.

[mermshaus]

I liked Zotero better than I'd have expected when I tested it a few weeks ago.

In OpenOffice Writer, it seems actually *possible* to manage and update your citation sources (even when using a footnote-based citation style) and bibliography with Zotero. (Honestly, I can't say that about other free -- at least "as in beer" -- tools in regard to OpenOffice.[1]) The created content blends smoothly with Writer's style system and it's easy to keep a document in sync with your bibliographic database.

The plugin for Writer is still in beta, though.

Besides that, I also think that it feels rather strange and somehow unnecessary to manage your bibliography from within a browser. (Well, I guess there are some advantages. Easy installation and portability for instance.) I'd also prefer some kind of central ISSN lookup service to grab the information in comparison to Zotero's "page scanning" / micro formats approach. But I haven't really tried to test this feature as most of the literature I use is written in German and I tend to enter all needed data by hand.

Which leads me to my major complaint: It's as much fun to use the Zotero browser GUI as it is to use Firefox' default bookmark manager. Which is none. Two annoyances: I have not been able to move multiple selected items to a different category at the same time (which might be entirely my fault). I have not been able to tag multiple selected items at the same time (which might be entirely my fault, too). Not being able to perform these easy tasks in a convenient manner is a show stopper.

Collaborative features (storing your database online!) would also be nice (seems like they're working on that). So, Zotero is by no means perfect but it's got a lot of potential to become a really useful tool.



[1] I guess I should finally start using a WYSIWYW system.

[Brian96]

So far I really, really love Zotero. I've always just managed references by hand, though, so I've nothing to compare it to. I'm glad I found it before I started on my dissertation.

As nearly as I can tell, though, it still is not compatible with Ff 3, and as this is the default browser in Hardy, I've decided to postpone upgrading until this is resolved. (It works out pretty well, really, since I don't actually have time to upgrade now anyway.)

[urgnom]

So far I really, really love Zotero. I've always just managed references by hand, though, so I've nothing to compare it to. I'm glad I found it before I started on my dissertation.

As nearly as I can tell, though, it still is not compatible with Ff 3, and as this is the default browser in Hardy, I've decided to postpone upgrading until this is resolved. (It works out pretty well, really, since I don't actually have time to upgrade now anyway.)
Well, the next update is going to work with FF3. If you download the developer snapshot it works very well with FF3 (and integration with OOo Writer if you are using that).

[frbe0101]

I was loving it for hte last few weeks, just drop citations from zotero to my OO documents using hte plugin, it was wonderful as before I jsut managed citations by hand and that was becoming a huge pain. but now that I upgraded to firefox 3.0 it does not work anymore, I got to wait for them to make a firefox 3.0 version!

[Brian96]

Well, the next update is going to work with FF3. If you download the developer snapshot it works very well with FF3 (and integration with OOo Writer if you are using that).

Yeah, I saw that the next update will be fully compatible. Any idea when the formal update is due? Or, are there any issues with using the development snapshot (I'm not real interested in a "beta" experience)?

[samden]

I was loving it for hte last few weeks, just drop citations from zotero to my OO documents using hte plugin, it was wonderful as before I jsut managed citations by hand and that was becoming a huge pain. but now that I upgraded to firefox 3.0 it does not work anymore, I got to wait for them to make a firefox 3.0 version!
You can always just install Firefox 2 in the meantime. It is available in Synaptic.

[sloggerkhan]

I had it installed once and didn't really understand how to use it.

[Brian96]

I had it installed once and didn't really understand how to use it.

I had trouble with it at first, too. Watch the flash demos at zotero.org and it walks you through it step by step.

[timbosity]

Just a not here. The dev version of zotero works quite well with ff3. Not glitches thus far... And the OO plugin is sweet:)

[hugmenot]

Zotero’s continuously updated development snapshot is compatible with FF3.

http://www.zotero.org/download/dev/zotero-trunk.xpi

(but it might be too bleeding edge for you, so caveat emptor)

[frbe0101]

Oh I fix it by hacking zotero (its on their forum) to make it think its compatible with FF3, so far it works perfectly, I'll upgrade to the next version that is truly qualified for FF3 when it becomes available.

I love it, I sync the references between my Home PC (winXP) and my Laptop (Ubuntu 8.04), adding citations is so dam easy now! The only complaint is it lacks the formate library of endnote, but I'm sure I could fix that if needed (IEEE is fine for my needs for now).

[Brian96]

Oh I fix it by hacking zotero (its on their forum) to make it think its compatible with FF3, so far it works perfectly, I'll upgrade to the next version that is truly qualified for FF3 when it becomes available.

I love it, I sync the references between my Home PC (winXP) and my Laptop (Ubuntu 8.04), adding citations is so dam easy now! The only complaint is it lacks the formate library of endnote, but I'm sure I could fix that if needed (IEEE is fine for my needs for now).

Out of curiosity, how are you syncing your references?

[frbe0101]

Well I told zotero to store all it citations in a folder, then I copy and past that folder between my computers (actually I use a sync program to sync the folders) so there are two identical folders on both computers that are synced regularly.

[Brian96]

Well I told zotero to store all it citations in a folder, then I copy and past that folder between my computers (actually I use a sync program to sync the folders) so there are two identical folders on both computers that are synced regularly.

Gotcha.

I am looking forward to Zotero's own server-synching, which according to the development roadmap, should be out in June.

[Brian96]

For the record, the version of Zotero now available on the zotero.org website (but not the one on the Ff add-ons site) supports Ff 3.0.

[orduek]

I have to say I checked bibus and Jabref but none of them was easily synced with OO's writer.
After adding Zotero I'm just thrilled! Its great for my needs, easy to add articles (through that button in the address bar) and easy to add citation with OO (through the extension).
And I find it better than Endnote.

[sybille]

I've added a page about the Zotero reference manager to the Ubuntu community wiki:
https://help.ubuntu.com/community/Zotero/

In addition to discussing how to install Zotero and the Zotero plugin for OOo, there are some tips on full-text indexing and note-taking that I hope will be useful for Ubuntu users.

[Frenske]

Looking for bibliographic software I stubled upon this thread! Oddly nobody mentioned pybliographer. It appears to support Open Office and the database seems based on bibtex. Anybody tried this one?
I have read somewhere the OpenOffice is developing it own bibliographic software.

[sybille]

For me, the major problem with Pybibliographer is that it doesn't support a lot of citation formats, or at least, not the ones I need. See:
http://en.wikipedia.org/wiki/Comparison_of_reference_management_software#Citati on_styles

Pybibliographer also doesn't have some of the features like file attachments and note-taking.

But it's definitely worth checking out - everyone has a different research style and therefore different needs, and I'm sure that it's just the right tool for some people!

[Brian96]

So, I've been doing a lit review, and today EBSCOhost's interface has change. That was startling in and of itself, but the problem is that Zotero no longer detects fields on the site (nor does it put the article or folder icon in the address bar).

Anybody else have this problem? Anybody find a solution?

[jraab22]

I don't use that particular site (EBSCOhost) but let them know over at zotero that there has been a change to it and they should fix it pretty quickly. This sort of thing unfortunately happens whenever a site changes the way it runs, just takes a couple of days for zotero to catch up.

[alperyilmaz]

hi,
I'm using Ubuntu 8.04. I'm running MS Office with Wine. I installed Zotero Firefox plugin. I also installed the Word .dot file for Zotero. But of course, Word cannot access Firefox since it's behind Wine. Does anybody have similar setup and successfully used Firefox-Zotero-Wine-Word all together?

[sybille]

hi,
I'm using Ubuntu 8.04. I'm running MS Office with Wine. I installed Zotero Firefox plugin. I also installed the Word .dot file for Zotero. But of course, Word cannot access Firefox since it's behind Wine. Does anybody have similar setup and successfully used Firefox-Zotero-Wine-Word all together?

I think you'd need to install Firefox for Windows in Wine, too.

But why not use OpenOffice.org Writer instead of Word?

[darwinev0lved]

I've tried asking at the Zotero forums but got no response from the Devs there just yet.
Has anybody else had this problem, or know what might be causing it and even better be able to fix it:
you should be able to drag a file e.g. a pdf onto a reference and Zotero save a copy of the pdf linked to that reference. But it just won't work.
I'm a new switcher from Windows, so my Ubunutu knowledge is non-existent: its either an Ubunutu or Zotero bug and I was hoping that it was a simply setting I need to alter in Ubuntu.
Thanks,
Jon.

[alperyilmaz]

Installing Firefox for Windows didn't help too much. After installing firefox, the error message changed into "cannot open macro storage". I think I get one step closer..

I used OO Writer and it was not good enough for me..

[sybille]

I've tried asking at the Zotero forums but got no response from the Devs there just yet.
Has anybody else had this problem, or know what might be causing it and even better be able to fix it:
you should be able to drag a file e.g. a pdf onto a reference and Zotero save a copy of the pdf linked to that reference. But it just won't work.
I'm a new switcher from Windows, so my Ubunutu knowledge is non-existent: its either an Ubunutu or Zotero bug and I was hoping that it was a simply setting I need to alter in Ubuntu.
Thanks,
Jon.

It doesn't work for me, either, Jon, with Zotero 1.0.7. I don't think it's a setting in the OS.

Have you tried running Firefox from a terminal after enabling debug output in Zotero (http://www.zotero.org/documentation/debug_output), and then trying to drag and drop? Maybe there will be some relevant output that you could post to the thread at the Zotero forums. I think that's the best place for it.

Also, I think you have the 1.5 beta installed - does it occur there, also, and is the debug output the same?

[orduek]

It doesn't work for me, either, Jon, with Zotero 1.0.7. I don't think it's a setting in the OS.

Have you tried running Firefox from a terminal after enabling debug output in Zotero (http://www.zotero.org/documentation/debug_output), and then trying to drag and drop? Maybe there will be some relevant output that you could post to the thread at the Zotero forums. I think that's the best place for it.

Also, I think you have the 1.5 beta installed - does it occur there, also, and is the debug output the same?

any solution on this matter?
the main reason to use MS Word is because I frequently sending drafts to my supervisor and it creates a problem of formatting etc.

[orduek]

up

[LFMZZ]

This is an old thread so I wanted to chip in on my experiences with Zotero:
I have been using Zotero for several months now, I have only used the beta version.
Pros
Synchronization
I set up a Box.net account since the Zotero storage was so limited. Works perfectly I have successfully synced my references across different computers and OS. They are also saved locally so I can access them even if I am offline (I have a stationary and a laptop at work with Windows and I have a Windows stationary and an Ubuntu laptop at home).
Browser integration
I have read a few comments about how the fact that Zotero lives in a web browser is an undesirable thing.
I can't understand that. Today most references are grabbed online, it is fantastic that with a click of a button I get my PDF file saved automatically, my www reference, or even book details.
The only downside is that it only works on Firefox and there are no plans to extend it to other browsers.
Office and Open Office plugin
Works like a charm, much easier to manage/edit than Reference Manager (which is what I was using before).
Stability
Never seen it crash, it doesn't mean that it wouldn't, but I have been using it heavily in the last 3 months as I have been writing a Review article.
Cons
Zotero has one HUGE and dangerous CON, that you might not notice until the very last minute when you are proof reading your paper before submission.

Journal names. I don't know how/where Zotero gets the journal names, but frequently in the field that should contain the full journal name, the name is written in abbreviated form, or in all caps, or in some way incorrect.
Then, the field that should contain the abbreviated form is often empty.
If you choose a style where the journal name should be the abbreviated form, you are totally screwed.
You have to go back to your references and check them one by one and correct them manually.
More so, there is no way of telling Zotero that you want your journal abbreviations to be followed by a point or not.
In the rare instances that both full journal name and abbreviated name fields are correct and complete, Zotero cannot set a point after the abbreviated word or remove it automatically. You have to check each reference manually and either:
1- change the abbreviated form and add/remove the point.
2- fill the alternative abbreviated form into another field and modify the citation style to grab the information from this other field.

This is a really bad issue, there are no warnings when you start using Zotero about it and since is a more or less random event (most likely related to where you grab your papers from, but I haven't tried to recreate the possible scenarios), you might not notice at first that the Journal names are incorrect.

I had a moment of panic when I finished writing my article and proceeded to check whether the references were alright and complied with the Journal specifications and found out about the disaster. It was really hard to find information about it in the forums and I really didn't have time to ask for help.

I still love Zotero, and hope they fix this huge problem soon.