Zotero extra / Bibtex note - how not to show?

gregsharp

Hi, wow, I'm really impressed with zotero. It is like the application that I didn't know I needed, but now I couldn't live without.

I have a question, maybe zotero, maybe bibtex.

I've found that zotero puts the PubMed PMID into the "extra field", which is converted to a bibtex note field. I do not want to clutter my bibliography with PMID's, but they are nice to have in the zotero database. I use a custom bibtex style created with makebst (I'm not an expert in this, but trying my best). I look through the makebst output (dbj file), and cannot find how to tell the style not to show the note field.

So, as you see, I am about to delete all these nice PMID's that zotero gave me. Any recommendations how to solve?

CB

I use bibtool (http://www.gerd-neugebauer.de/software/TeX/BibTool.en.html) for cleaning up various aspects of Zotero's bibtex output (it can alter capitalisation, choose which fields to include, sort, etc), and creating my desired key format.

There are no binaries available for Windows, but it compiles easily under cygwin (or of course Linux or OS X).

Bibtool's config file syntax takes a little poring over, but once you've got it, it makes for a nice easy workflow: export collection from Zotero -> run bibtool. It would be even easier if Zotero allowed you to automatically run external tools on exports.

gregsharp

Hi CB. Thank you for your suggestion.

I tried bibtool, but it is not easy. It does not seem to be actively maintained. For example, it does not compile out-of-the-box for me on cygwin. I looked at the configure script, and it does not seem to be updated for cygwin's relatively modern version of tcl.

Or maybe there is a newer version somewhere else? The one on the web page is 2.46.

CB

Sorry, you're right, I included the wrong link. 2.48 compiled on cygwin without modification for me, and is available on CTAN (or linked from http://www.gerd-neugebauer.de/software/TeX/BibTool/).

I get the impression that it isn't really maintained, but I haven't come across bugs so far (though I only use a fraction of its functions).

gregsharp

Thank you. This one builds just fine. I was even able to create a native binary using -mno-cygwin.

CB

Reciprocal thanks for pointing out -mno-cygwin, which I hadn't come across before. I'm happy enough using cygwin, but it's very handy to have a windows executable that's easier to launch from other windows apps.

scot

I'm also glad to know about bibtool for exactly the same reason. BibTeX sytles in general seem to be designed to "make use of everything in the database that they have a place for", so "extras" "doi" "isbn/issn" and "url"s all make their way into my biblio currently (using biblatex and the chicago-notes style). They don't seem to think that you might want to keep the data, but not cite it at every chance.

CB

scot: exactly, that's the reason that got me using bibtool in the first place. 'Extras' and having the month in the date drove me nuts. I couldn't find a way to turn them off in BibTeX, and I didn't want to delete data just for display purposes.

Actually I find BibTeX pretty dreadful, and I've never found the time to understand it. People swear by it and LaTeX, but from a UI perspective they're dreadful tools, but when the main alternative is the truly egregious Word/OO, I see little choice for the time being.

hairyson

@gregsharp (or anyone else able to respond): I run WinXP and would love a compiled version of bibtool, but I have no compiler or skill in that regard, and no cygwin. Can you (or anyone...) publish or email to me or link to a compiled version?

I will use it as a custom tool within TeXnicCenter if it works well enough.

Cheers!
Ben

CB

Ben, email me at bibtoolzotero@mailinator.com and I'll send you a copy.

hinnerk

There is a way to change the bst-file to ignore the content of the note field: Just edit the bst-file, search for "FUNCTION {format.note}" and replace the adjacent "note empty$" with "#1". The new function declaration should look similar to this:

FUNCTION {format.note}
{
#1
{ "" }
{…}
if$
}

(That means "note fields are always empty". :-)