Posts Tagged ‘bibliographic management’

Citation management means different things to different people

August 3rd, 2011

I got to talking with a mathematician friend about citation management. We came to the conclusion that “manage PDFs” is my primary goal while “get out good citations” is his primary goal. I thought it would interesting to look at his requirements.

His ideal program would

  1. Organize the PDFs (Papers does this, when it doesn’t botch the author names and the title) preferably in the file system, so I can use Dropbox
  2. Get BibTeX entires from MathSciNet, ACM, etc. EXACTLY AS THEY ARE
  3. Have some decent way to organize notes by “project” or something

He doesn’t care about:

  1. Typing \cite
  2. A “unified” bibliographic database
  3. Social bibliographies (though I am not against them; it is just not a burning issue)

He says:

I guess the point is that, if I am writing something and I know I want to cite it, and I know there is a “official” BibTeX for it, I just need a way to get that more quickly than:

  1. Type the URL
  2. Click on “Proxy this” in my bookmarks bar
  3. Search for the paper
  4. Copy/paste the BibTeX
  5. Edit the cite key to something mnemonic

He followed up with an example of the “awful” awful, lossy markup Papers produces which loses information including the ISSN and DOI; he prefers the minimalist BibTeX. (oops!; he adds “I understated how bad papers is. The real papers entry (top) not only has screwy names, but junk instead of the full journal name. The papers cite key is meaningless noise too (but mathscinet is meaningful noise).”) To get around this, he does the same search/download “a million times”.

AMS Papers2 BibTeX:
@article{AR78,
author = {L Asimow and B Roth},
journal = {Trans. Amer. Math. Soc.},
title = {The rigidity of graphs},
pages = {279--289},
volume = {245},
year = {1978},
}

Papers' The AMS version of the same BibTeX:
@article {AR78,
    AUTHOR = {Asimow, L. and Roth, B.},
     TITLE = {The rigidity of graphs},
   JOURNAL = {Trans. Amer. Math. Soc.},
  FJOURNAL = {Transactions of the American Mathematical Society},
    VOLUME = {245},
      YEAR = {1978},
     PAGES = {279--289},
      ISSN = {0002-9947},
     CODEN = {TAMTAM},
   MRCLASS = {57M15 (05C10 52A40 53B50 73K05)},
  MRNUMBER = {511410 (80i:57004a)},
MRREVIEWER = {G. Laman},
       DOI = {10.2307/1998867},
       URL = {http://dx.doi.org/10.2307/1998867},
}

I’ve just discovered that BibDesk‘s ((See also A short review of BibDesk from MacResearch)) ‘minimize’ does what he wants: its has output is quite close to the AMS Papers2 version:

@article{AR78,
	Author = {Asimow, L. and Roth, B.},
	Journal = {Trans. Amer. Math. Soc.},
	Pages = {279--289},
	Title = {The rigidity of graphs},
	Volume = {245},
	Year = {1978}}

I’d still like to understand the impact the non-minimal BibTeX is having; could be bad citation styles are causing part of the problem.

While we have different needs for citation management, we’re both annoyed by the default filenames many publishers use – like fulltext.pdf and sdarticle.pdf. But I’ll tolerate these, as long as I can get to it from a database index with a nice frontend.

We of course moved on to discussing how research needs an iTunes or, as Geoff Bilder has called it, an iPapers.

This blog post brought to you by Google chat and the number 3.

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Posted in books and reading, information ecosystem, library and information science, scholarly communication | Comments (0)

Papers2 does not integrate with external iPad applications in the way I expected

July 31st, 2011

Papers2 does not integrate with external iPad applications in the way I expected. I use iPad applications like GoodReader, iAnnotatePDF, and PDFExpert to read and annotate papers.

The functionality I expected was:

  • Export from Papers to an external PDF annotation application
  • When I reopen Papers, the annotated PDF is shown in my library

However, here is what happens:

  • Export from Papers to an external PDF annotation application. It renames the file, using a random string as the filename.
  • When I reopen Papers, only the original (unannotated) PDF is in my library.
  • Alternately when I export from the external application, the annotated file is imported as a *new* PDF, unconnected to the original, with a random string used for the filename.

I started using Papers because managing filenames in iAnnotate wasn’t working: I couldn’t figure out which files were which. So this is absolutely key for me.

==

This is a bug report to Papers2, copied here since bug reports are private. Any workarounds or suggestions for alternate annotation/reference management workflows would be very welcome.

This annotation environment completely failed to meet my expectations: I expected to ‘Open In’ an annotation application; in fact there’s just ‘Export’ and ‘Import’, meaning that the annotated file isn’t automatically stored in the Papers2 library.

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Posted in books and reading, iOS: iPad, iPhone, etc. | Comments (1)