Please hold my hand...

bothide

I have been looking around for quite some time for a solution that is able to handle and process the thousands of scientific papers that I have collected over the years and stored as individual pdf files in a directory of my Unix/Linux computer. The solution/software in question should, preferably, be able to create an easily searchable database and at the same time generate entries in my .bib database. If it would be able to do this automatically by extracting information from my pdf files, it would be even better.

When I asked around I was recommended to try zotero. But after installing it I am lost. There is no way I can find out what zotero is supposed to do or how to do it. Personally I find the user interface cryptic and counterintuitive and the on-line help is of no use for me since it not written for beinners/newcomers but seems to require quite an amount of pre-knowledge on what zatero is and how it works.

If somebody has some neophyte experience to share, I would appreciate it immensly. All I want to do is to see how zotero works to judge whether it is of any use for me or not...

Thanks.

noksagt

Personally I find the user interface cryptic and counterintuitive and the on-line help is of no use for me since it not written for beinners/newcomers but seems to require quite an amount of pre-knowledge on what zatero is and how it works.

Some pages, such as:
http://www.zotero.org/support/quick_start_guide
http://www.zotero.org/support/screencast_tutorials
are intended for newcomers. Is there something specifically that you're hung up on?

adamsmith

problem is, there is not a good help page for people starting out with a large chunk of pdfs, but this may help:
http://www.zotero.org/support/retrieve_pdf_metadata

Also, LaTeX related functions are not well documented at the beginner level, simply because LaTeX folks tend to not need it - you can easily export Zotero to bibtex, though.

bothide

After being a TeX/LaTeX "power user" for over twenty years, I have no problem with the typesetting. I have managed to get a pdf file into zotero but it was not straightforward. I even managed to produce a BibTeX entry from it but don't approve of the style. So I need to find a way to change the BiBtex entry style settings... Still I am quite confused and have, for instance, not been able to find out what the zotero database is called and where it is stored. Syncing between two computers is still a mystery. But I will continue for a little while longer before I decide to use zotero or to give it up.

A simple question, when I have brought up zotero at the bottom of my Firefox window, which icon shall I click to go to the Zotero web site?

Bo

dstillman

Bo: Frankly, I'm not sure why people would be willing to "hold your hand" (other than due to their extreme patience and generosity) if you're not willing to put in even a modicum of effort on your own.

Still I am quite confused and have, for instance, not been able to find out what the zotero database is called and where it is stored.

Searching Google for "zotero data" would take you to the Zotero Data page. Searching for "zotero database" would take you to the DB Repair Tool, which also tells you how to find your Zotero data directory.

Syncing between two computers is still a mystery.

Searching Google for "zotero sync" would take you to the sync documentation. If you have questions that aren't answered in the documentation, you'd have to tell us what those were.

Looking in the Zotero preferences would also reveal both of these things.

A simple question, when I have brought up zotero at the bottom of my Firefox window, which icon shall I click to go to the Zotero web site?

Double-click the relevant library ("My Library" or a group) in the left pane of Zotero. But this will only work if you've actually synced.

adamsmith

changing bibtex output is non-trivial, so that might be a show stopper for you.
(Zotero uses a javascript file to create the bibtex, you'd have to change that).
the zotero database is explained here:
http://www.zotero.org/support/zotero_data
(it's the 3rd search result when you search the documentation for "zotero database" - that really doesn't seem so bad).
You can find the bibtex.js in the translator folder within that Zotero data folder in case you do want to modify it.

[There is no icon to go to the Zotero page from Zotero - in normal usage of Zotero the webpage has no role - though I think there is a getting help menu function that gets you to the forum. edit: what Dan says]

Syncing really is easy - click the sync icon (the green arrow on the top left) fill out the sync information when prompted (same username and password as forum) - done.

Getting a pdf into Zotero is usually by drag&drop from the file system - i.e. as easy as it gets. That's broken under linux, so that makes things a little iffy (use "store copy of file" in the green plus menu in case you hadn't found it.

I'm not sure why Zotero isn't intuitive to you - most new users see that as it's greatest strength - but maybe long experience with non GUI software actually makes things harder - but then, why would you not just use jabref?

bothide

Thanks for all the help. With the "mystery of syncing" I meant the inner workings - not how to execute it (which is really trivial). With some guesswork I now think I understand that the copies of my pdf files are stored locally on my computer (in the Mozilla tree) and not remotely on a zotero central server somewhere. That explains why I was unable to the sync zotero archives (libraries? collections?) that I stored when I ran my laptop in linux after rebooting it in Windows, but was able to sync with another computer.

Drag and drop doesn't seem to work as expected for me (in Linux) but, again, it may be that I haven't been able to understand the zotero philosophy yet...

What worries me is how to modify the BbTeX output. The default output does not conform to de-facto standards among "power" LaTeX-ers and from the very few zotero generated .bib files I have been able to check, the output seems to be buggy (not leaving certains things to the bibstyle). It would be nice if zotero could provide a simple way (GUI?) to edit the output style.

Also, if I understand correctly, the "Link to File" or "Store Copy of File" only work for one single (pdf) file at the time, and I have many thousands... Please correct me if I am wrong.

But I must say that my first impression is overall very good. However, being a Unix (and lately Linux) diehard with 25+ years of daily Unix exposure, I get the feeling that the user interface is very non-Unix and more Windows-like. For me that is counter-intuitive. For others I am sure it's quite natural.

Thanks once again

Bo

noksagt

The default output does not conform to de-facto standards among "power" LaTeX-ers and from the very few zotero generated .bib files I have been able to check, the output seems to be buggy (not leaving certains things to the bibstyle).

What specific issues do you have?

adamsmith

Also, if I understand correctly, the "Link to File" or "Store Copy of File" only work for one single (pdf) file at the time, and I have many thousands... Please correct me if I am wrong.

you're wrong ;-) You can select bulks - since, as I mention above, file drag&drop is broken in Linux, that's the only way to get large number of files into Zotero in any reasonable amount of time.

bothide

Good to hear that it is possible to select bulks. Still have to find out what "bulks" means. Tried a tarball with a dozen or so pdf files in it but that didn't work...

noksagt

Shift-click or ctrl-click in the file picker & you can select multiple files.

bothide

That was the first thing I tried (in xubuntu 10.04) but nothing happened. It turned out that I did not wait long enough. Now I got that working. Slow but faster than picking files one by one.. Thanks!!

bothide

One more thing. Now that I have downloaded a large amount of pdf files, I would like to extract metadata from all of them in one go. Haven't figured out how to do it - if at all possible...

noksagt

You should do them in reasonably-sized batches. You can, again ctrl or shift click multiple records, right-click & select "retrieve metadata for pdfs"