Zotero notes

These are some notes from @rjleveque regarding attempts to use Zotero to manage references, with the goal of creating an online database at https://www.zotero.org/groups/clawpack that will be of use to the broader Clawpack community.

I am using the stand-alone Zotero on a Mac, and use the Chrome plug-in for downloading new references from the web. If you join the Clawpack group at the link above, you should see it show up under Group Libraries on your own Zotero. You can drag items from it to your library or vice versa.

Note: The items currently in this group library are things I pulled down while searching recently for papers citing GeoClaw, and most of them have messed up metadata that needs to be fixed up.

There are some things I like very much about Zotero and some things that seem difficult, particularly in relation to using this as a database in connection with bibtex. I've started using better-bibtex, https://zotplus.github.io/better-bibtex/index.html which helps some, in particular so that I could control the cite-keys it generates.

If we want to have a shared it would be very useful to agree on what format we want to use for bibtex cite-keys, since these are needed when you export from Zotero to bibtex and should agree with how we want to cite things in latex documents. I generated cite-keys for all the papers now at the link above, which you can see if you click on a paper and look at the "extra" field. I chose the format in which the first two authors names are concatenated along with the year. Does this seem ok? To change this in your stand-alone Zotero,

Zotero preferences -> Better Bibtex
citation key format:  [authors2][year]

See http://jabref.sourceforge.net/help/LabelPatterns.php for other options.

If you select one or more papers in your zotero library and then right-click and "generate bibtex key" it will auto-generate the key in the "extra" field so you can see what it will be.

If you select papers and hit Cmd-Shift-C it will copy something to your clipboard for each paper that can be pasted elsewhere. What it copies is set by:

Zotero preferences -> export -> output format 
  select "Better Bibtex"  so Command-Shift-C grabs bibtex entries
  select "LaTex citation"  so Command-Shift-C creates \cite{...}

In principle from the Shortcuts tab in preferences you can set Cmd-Shift-A to do something different than Cmd-Shift-C but I couldn't get this to work.

Another issue I've run into is that capitalization in titles is not handled properly when exporting to bibtex. If you change the metadata title to include braces as you would in bibtex, e.g. "Velocity Measurements Near {Hawaii} Compared to Model Simulations of the 11 {March} 2011 {Tohoku} Tsunami", then exporting from Zotero will change all the braces to \{ and \}, and then it gets typeset in LaTeX with braces appearing (but no caps). But it turns out if you give the item the tag #LaTeX in Zotero, then it exports the title verbatim, see https://zotplus.github.io/better-bibtex/.

Zotfile seems useful to have Zotero store everything where you want it to, e.g. in a directory under Dropbox. Then it's easier to view your pdf files from another device, and apparently also use Zotero on an iPad or iPhone using Zotpad, e.g. to mark up pdf files with iAnnotate.