Saturday, April 09, 2011

Hmm - How did I miss this paper discussing RFAM, Wikipedia & community annotation #cool

Edits for Wikipedia articles on RNA families. The cumulative number of edits since 1st January 2007 for the 733 Wikipedia articles that are associated with Rfam entries is shown in black. The total number of edits that were reverted or labeled as vandalism is shown in red. To mid-2010, there were just 106 of these. However, some reverted edits may have been well-intentioned but were deemed inappropriate for Wikipedia. From
Very interesting discussion in this paper on Rfam about community annotation: Rfam: Wikipedia, clans and the “decimal” release. In the paper the authors (inlcuding Alex Bateman, Sean Eddy, Paul Gardner and others) discuss the use of Wikipedia for Community Annotation of biological databases. They report:
Given our positive experiences, we can highly recommend other curation efforts turning to Wikipedia for their annotation
I am not sure how I missed this paper when it came out recently.  But it is definitely worth a look.  The last line hints at future developments
We look forward to working with the wider community to develop these new tools and techniques.
It seems that they have bought into the Wikipedia based annotation system as having enormous potential.  I generally agree though I am not sure how this is best done.   


  1. PFam has recently started using Wikipedia articles as well. They also changed there license from GNU GPL to Creative Commons Zero (i.e. public domain).

    Hard to say if wiki is the best solution for annotation. However, if a wiki is going to be used I am glab when people use Wikipedia.

  2. I've seen various wiki-based community annotation projects arrive, and been directly involved in a couple. I have also seen most die, for want of an engaged community. Pfam's genius is to go way beyond adopting an existing open wiki software by buying into the entire open Wikipedia community. If this works (and I'm hopeful) expect many imitators.

  3. @whsqwghlm "Pfam's genius"? What?

  4. mmm, this article on Nature Precedings can also be interesting for you:
    Mietchen et al, Wikis in scholarly publishing. Available from:

  5. That should, of course, have been "Rfam's genious". Sorry Paul.


Most recent post

My Ode to Yolo Bypass

Gave my 1st ever talk about Yolo Bypass and my 1st ever talk about Nature Photography. Here it is ...