Organizing Shared Libraries of Articles

I'm trying to figure out the best way for a group of people to share libraries of articles.  It'd be nice if each user had some ability to adjust it to their style, and it's probably important to make it really hard for anyone to Jar-Jar the whole thing.  Also, it'd be cool if it was integrated with some citation software, and maybe a useful note-taking system (NVivo or Atlas, or maybe just PDF annotations?).

So here's things I want to remember to look into:

• Zotero group libraries - are attached PDF's easily downloadable?
• Scripts
• It'd be easy to make one to periodically copy items from Dropbox folders to whatever each user prefers to use (but that'd be easy to Jar-Jar).
• I think there's also ways to use an Endnote library to rename files in a given format, like "Author (year) - title."  That'd make it easy to incorporate everyone's folders after they depart.
• Endnote Web
• Google Reader
• Binders with printed articles

UPDATE - 09-01-11

I just saw this on a Mendeley feedback forum:

Mendeley's database is a SQLite file and you can export your library with file attachment links to Bibtex, RIS and EndNote XML and other projects have built tools that can interoperate with them.

Making use of these export facilities, one way to get metadata from Mendeley Desktop into PDF files as XMP metadata is as follows:

1. Select documents in Mendeley Desktop and go to File -> Export. 

2. Choose 'Bibtex' as the file type 

3. Open the Bibtex file in JabRef 

4. Go to 'Tools -> Write XMP Metadata to PDFs'

See http://jabref.sourceforge.net/help/XMPHelp.php for more details.

Be aware that if you are syncing files with Mendeley Web these changes to the PDF files will not be mirrored to other PCs.

so maybe that's something to try. 

New Journal, New Citation Style

I apparently thought this was the sort of thing that was too obvious to write down, but I just spent 20 minutes looking it up again.  So here we go.

Endnote
1] Download it (endnote styles end in .ens)
2] Put it in Applications-> Endnote -> Styles
3] Ta freaking da

Or, in Zotero
1] Download it (I don't know formats it'll take, but I'm sure there's a list easy to find somewhere)

also 1] Or do the Endnote version above, and then...
2] In Zotero click the Gear -> Preferences -> Styles -> click the Plus
3] Ta freakin da.

Although this didn't work on my last attempt.  The forums told me that it's not really that great a process (going through Endnote to get a new style), and that I should probably wait for their CSL editor.  They also said that CSL (citation style language) is more powerful than the way Endnote does it.  I'm not sure how, but something to think about.

Mendeley?

Mendeley is cool.  Wizfolio might be cool.  The name is not as cool.

Things I learned setting up Mendeley -

• It'd probably be better to import from a program, and then attach all the PDF's.  Or just do the PDF's and fix all the citations.  Either way, you'll have to fiddle with most entries.  I tried to do both, for completeness, and I not only get to change most of them, but I get to delete multiple versions of each one too.
• 500 Mb isn't as much as I thought.
• I think items can be in more than one folder at a time without actually being duplicated - but this might only be true for certain folders like "Recently Added," "Zotero Library" or "Favorites" or whatever.  I'm not sure about user-created folders.
• Tags don't import very well from Zotero.
• Although the syncing with Zotero is continuous, it won't reimport all the articles if you move them somewhere else.  It will only bring in the new ones (Cool!)
• PDF edits and notes are only saved in Mendeley unless you intentionally export them to the PDF.  They can still be shared with others through Mendeley.
• Citation plug-ins are iffy.
• One-click add actually works in Chrome, although it's slow.  You have to go get the PDF on your own.  I don't think this is likely to change, as I suspect there are some licensing issues with freely distributing copies of copyrighted material.
• You can't link PDF's to public groups, for example.  Actually, that's my only example.  It's the whole reason I think there's an issue.

Editing Styles in Zotero

Use this page.  It actually isn't that hard, although it requires a lot more thinking than the similar Endnote process.

Having said that it didn't work the first few times.  Here's some stuff I may have learned:

• for TextEdit you should save it as Unicode-16, I think.  I have no idea what that is, but it didn't recognize the file type when it was Unicode-8, despite the .csl extension.
• You can also add styles (or delete them) through the Style Manager.  Click the gear icon in Zotero, pick Preferences, click Styles tab.
• I think if, when you rename the file, title and id that there are length limits.  So "American Psychological Association 6th Edition Single Spaced" didn't work, but "APA6singlespace" did.  I'm also not sure if spaces are allowed.

This page explains the language the citation styles are written in, a bit.

Let's Get Zotero

The title is like that Black Eyed Peas song.

Step 1:  Update Firefox to the latest non-beta (right now that's 3.6)

• It's easier to do this using some other browser.  It's also slightly antisocial.

Step 2: Download the latest Zotero that's non-beta (right now that's 2.0.9)
Step 3: Go here and follow the steps

• If you're using a Mac, you'll have to install a Python extension and the Word plug-in

Step 4: Import a library?

• If you want to do this be smart about it so that it doesn't turn all radioactive fish on you with tags and eyes and html attachments everywhere.  Maybe I'll post about it later.  Otherwise do the Google.  

Zotero?

I'm trying out Zotero.  Here are my thoughts.

• The tags were stupid, and it was a pain to get rid of them.
• Should I use tags or folders to organize it all?
• Why can't I move articles from a group library to "My Library?"  something to remember.
• I really like that when I change something in the Firefox window (add something to a group, change the publication year, etc) it updates immediately in the Word plug-in window.
• Attaching pdf's of articles:
• The "Attach stored copy of file..." option is cool, but I need to see if it allows me access to those files from another computer.  It's annoying though because it grays-out the articles with attachments in the "add citation" dialog window, and makes each entry two lines.
• The "Attach link to file..." doesn't do those annoying things in the "add citation" window, but I doubt it will let me access the file from another computer.

UPDATE:

I asked on the forums about those expanded things in the "add citation" window.  They were very helpful. The problem is that the search function I use to sort the citations is a "full text search" so it's showing me that whatever search terms I typed (usually an authors name) show up in the citation AND in the attached PDF.  Pretty cool function, the full text search is really fast, but it's annoying for this purpose.  They recommended just sorting by the Author's column and "starting to type."  That will be quick and easy.

Tags in Zotero

There are too many stoopid tags in my Zotero library.  I think there's some way to import from Endnote that doesn't include them, but...I'm not into that right now.

So, this forum exists, and it's good.  This is a list of things I didn't understand for a while:

• You have to go Preferences (the little gear) - Advanced - "Show Data Directory" to find out where the SQL thing is.
• I don't know one thing about SQL.  Not even one thing.
• The commands listed have to be executed separately, and they're wrong in the post:

delete from itemTags where itemTags.tagID in (select tags.TagID from tags where 

tagType = 0)

delete from tags where tagType = 0

• "tagType" doesn't exist, so change it to just Type.
• I picked a few tags that I liked and changed their "Type" to 1, so that I could save them.