Uploading Your Theis Literature Review to Wikipedia

- - posted in bioinformatics

Every PhD student can contribute to open science by uploading their thesis literature review onto Wikipedia!

My thesis was entitled “Phage-host evolution in a model ecosystem”, where I tracked the evolution of phage genome evolution and the evolution of bacterial defense mechanisms using metagenomics. When I was writing my thesis I spent a lot of time writing up the section on CRISPRs, which are a type of bacterial adaptive immune system. The CRISPR field has exploded in recent times due to its applications for genome editing which has also meant that there have been numerous great reviews on the ever expanding primary literature. Despite this though I found the CRISPR page on wikipedia to be a bit bare (of course now that I’ve updated it things look better, but check out the edit history for a look at what I’ve added). Since there was already a saturation of reviews on the subject I decided to go through and add in what I had written for my thesis to wikipedia. By far the most important and difficult part of this is was formatting the references right. So I made a simple workflow for getting what I wanted out of my thesis and into wikipedia.

  1. First thing, I wrote my thesis in word and used endnote to format my references using the style from nucleic acids research (which is a numbered style). If you want to use my method you need to have the exact formatting style
  2. Export the literature review from word as plain text and then removed all the parts that aren’t needed
  3. Put back in some formatting for the headers using wikipedia’s markup
  4. Split out the bibliography into a separate file
  5. Then use some very dodgy perl code I wrote to format all of the in text citations into the format that wikipedia requires

This perl code takes the text and looks for numbers, or lists of numbers inside parentheses. For example: (1,2,5), (1-7,14), (1). Then looks up what those references are in the bibliography, extracting the title of the journal article. Then it looks up what the pubmed ID is for that paper using entrezdirect with the title as the search term. After getting the pubmed IDs for all the cited references it saves them to a file, so that it can be used later on (without looking up the pubmed IDs again) and any errors can be fixed manually. Finally all of those in text citations are replaced with the proper wikipedia markup and your ready to upload.

There are so many scientific wikipedia pages that are way too brief for their subject matter and I’m not just talking about the thousands of stubs for bacterial and archaeal species either. My current work is with methane seep sediment communities that perform anaerobic oxidation of methane (AOM), the wikipedia page contains five paragraphs. Looking at the broader topic of methanogenesis there is still only three short paragraphs on the biochemistry. We know so much more than this, all that knowledge fills the pages of hundreds of review articles yet when someone, anyone types anything into google the first match that comes up is wikipedia. We should make it better cause it’s ultimately the most visible publication on the internet.