A better system for referencing

DATE: 2018-11-25

AUTHOR: John L. Godlee

For a long time I was using Mendeley as a way of managing papers and references. However, the last few months I've found that Mendeley has been getting more and more clunky on my laptop, even with regular updating, and once or twice even doing an entirely fresh install. I also didn't like the idea of things not being in my control. After a recent report that I wrote, I got pulled up for dodgy referencing, this being because Mendeley is fairly inconsistent with how it labels things like author names, issue numbers etc.

I write all of my important work in LaTeX, so I generally exported my Mendeley reference lists to BibTeX files, so I figured I would cut out Mendeley completely and try to just hold my references in simple flat .bib files. Here is a sample of my master BibTeX file, lib.bib:

@article{brusa2014,
  author = {Brusa, A. and Bunker, D. E.},
  year = 2014,
  title = {Increasing the precision of canopy closure estimates from hemispherical photography: Blue channel analysis and under-exposure},
  journal = {Agricultural and Forest Meteorology},
  volume = {195-196},
  number = {},
  pages = {102--107},
  FILE = {~/Documents/papers/brusa_bunker_2014.pdf},
  DOI = { http://dx.doi.org/10.1016/j.agrformet.2014.05.001 }
}

@article{williams2017,
  author = {Williams, L. J. and Paquette, A. and Cavender-Bares, J. and Messier, C. and Reich, P. B.},
  title = {Spatial complementarity in tree crowns explains overyielding in species mixtures},
  year = 2017,
  journal = {Nature Ecology \& Evolution},
  volume = {1},
  number = {},
  pages = {1--7},
  FILE = {~/Documents/papers/williams_2017.pdf},
  DOI = { http://dx.doi.org/10.1038/s41559-016-0063 }
}

@article{sahin2016,
  author = {Sahin, C.},
  title ={Comparison and Calibration of Mobile Phone Fisheye Lens and Regular Fisheye Lens via Equidistant Model},
  year = 2016,
  journal = {Journal of Sensors},
  volume = {2016},
  number = {  },
  pages = {11},
  FILE = {~/Documents/papers/sahin_2016.pdf},
  DOI = { http://dx.doi.org/10.1155/2016/9379203 }
}

Whenever I read an article of interest, or want to save any reference for that matter, it goes in lib.bib. I normally keep notes for the articles I've read in a separate set of files related to whatever project I'm working on, so I search those to find references that I can't quite remember the details of. Papers are all stored in a papers/ directory which gets backed up regularly, it's just a flat directory. I suppose I could make it into a heirarchy based on theme, but I feel that would get complicated too fast, for example, if a paper should be included in two themes, or papers should be retro-actively added to emerging themes.

Typing all the BibTeX markup by hand is very laborious. I use Vim for text editing and I felt it was time to learn about snippets, which are just small chunks of customisable text that can be entered into documents by typing a keyword and hitting tab. I use the 'SirVer/ultisnips' plugin, which you can find here[1]. An example of a .bib snippet that I use to generate an article template:

1: https://github.com/SirVer/ultisnips

snippet article "Bibtex for article" b
@article{$1,
  author = {$2},
  title = {$3},
  year = $4,
  journal = {$5},
  volume = {$6},
  number = {$7},
  pages = {${8:1--10}},
  FILE = {~/Documents/papers/$9},
  DOI = { http://dx.doi.org/$10 }
}
endsnippet

The $1 codes are placeholders which are filled by the user, these placeholders can be quickly traversed using C-l and C-h. Some, like the page numbers, contain example text to remind me how to format certain inputs. Here is the snippet for a book:

snippet book "Bibtex for book" b
@book{$1,
  ${2:author/editor} = {$3},
  title = {$4},
  year = $5,
  publisher = {$6},
  address = {${7:City, Country}}
}
endsnippet

Here are the .vimrc settings I have for UltiSnips:

let g:UltiSnipsExpandTrigger="<tab>"
let g:UltiSnipsJumpForwardTrigger="<c-l>"
let g:UltiSnipsJumpBackwardTrigger="<c-h>"

let g:UltiSnipsEditSplit="vertical"

let g:UltiSnipsSnippetDirectories=[$HOME.'/.vim/Ultisnips']