http://www.eresearch.org.nz/event/eresearch-nz-2013

1. Engaging a Scientific Community in Contributing
to a Biological Database
Paul Gardner
June 21, 2013
Paul Gardner Engaging Scientists

2. What is RNA?
RNA is a fundamental biological molecule, essential for untold
biological processes
My aim is to build an analog to the Periodic Table for
classifying RNA families and motifs, enabling researchers to
predict function.
New technologies are accelerating the rate of RNA discovery.
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Paul Gardner Engaging Scientists

3. What is Rfam?
A database of ncRNA alignments and structures
Used for annotating RNAs in genome sequences, bioinformatic
algorithm development and molecular evolutionary analyses
Gardner et al. (2008) Rfam: updates to the RNA families database
Nucleic Acids Research.
Paul Gardner Engaging Scientists

4. How can we keep textual descriptions of RNAs up to date?
AC RF00005
ID tRNA
CC Transfer RNA (tRNA) molecules are approximately 80 nucleotides in
CC length. Their secondary structure includes four short
CC double-helical elements and three loops (D, anti-codon, and T
CC loops). Further hydrogen bonds mediate the characteristic
CC L-shaped molecular structure. tRNAs have two regions of
CC fundamental functional importance: the anti-codon, which is
CC responsible for specific mRNA codon recognition, and the 3’ end,
CC to which the tRNAs corresponding amino acid is attached (by
CC aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of
CC the genetic code in two manners: having more than one tRNA (with
CC a specific anti-codon) for a particular amino acid; and ’wobble’
CC base-pairing, i.e. permitting non-standard base-pairing at the
CC 3rd anti-codon position.
RN [1]
RM 8256282
RT The tertiary structure of tRNA and the development of the genetic
RT code.
RA Hou YM;
RL Trends Biochem Sci 1993;18:362-364.
RN [2]
RM 9023104
RT tRNAscan-SE: a program for improved detection of transfer RNA genes
RT in genomic sequence.
RA Lowe TM, Eddy SR;
RL Nucleic Acids Res 1997;25:955-964.
Paul Gardner Engaging Scientists

5. This Wikipedia thing looks pretty good!
Paul Gardner Engaging Scientists

6. WikiProject RNA
The WikiProjects are social corners of Wikipedia for interested
parties to discuss themed articles
Involved in reviewing, ranking and rating articles
Now rolled into the larger WikiProject Molecular and Cellular
Biology
Paul Gardner Engaging Scientists

7. How has the Wikipedia experiment gone?
x x x x
x
x
x x
x
x
x x x x x x x
x x x x x x x x
x x
x
x x x x x x x x x x
x
x x
x
x x x
0
2000
4000
6000
8000
10000
Number of Rfam pages edited
Year
Numberofedits
2007 2008 2009 2010 2011
9089
x x xxxxxxxxxxx xxxxxxxxxxxx xxxxx xx x
106
Total edits
Vandalism
Gardner et al. (2011) Rfam: Wikipedia, clans and the “decimal”
release Nucleic Acids Research.
Paul Gardner Engaging Scientists

8. Who are these Wikipedians donating their time?
Rfambot
Ppgardne
Citationbot1
WillowW
SmackBot
DOI_bot
Addbot
Alexbateman
Jebus989
JenniferRfm
Zashaw
Rjwilmsi
Qwyrxian
Yobot
RE73
Narayanese
RichFarmbrough
Addshore
Wgscott
MiRroar
RjwilmsiBot
Arcadian
DO11.10
Gortonk
Banus
Drmed36
FrescoBot
Boghog
Top 20 Rfam wikiproject editors
Numberofedits
0
200
400
600
800
1000
Bots
Proof Readers
Scientists
Paul Gardner Engaging Scientists

9. What incentives can we give to Academics?
Academics love publishing articles
Introducing the “families track” at RNA Biology
Publication requirements are an alignment & a Wikipedia
article
100s of new families have been added thanks to this track
Paul Gardner Engaging Scientists

10. Who else is now using this model?
Finn, Gardner, Bateman (2012) Making your database available
through Wikipedia: the pros and cons Nucleic Acids Research.
Paul Gardner Engaging Scientists

11. Wikipedia need you!
What is the highest impact contribution academics can make?
Rule 1: Register an Account
Rule 2: Learn the Five Pillars
ENCYC, NPOV, FREE, RESPECT, NORULES
Rule 3: Be Bold, but Not Reckless
Rule 4: Know Your Audience
Rule 5: Do Not Infringe Copyright
...
Paul Gardner Engaging Scientists

12. Who might be reading about your field?
Paul Gardner Engaging Scientists

13. Thanks!
The Rfam Consortium
Wikipedians & the long
tail!
PPG is supported by a Rutherford Discovery Fellowship from Government funding, administered by the Royal
Society of New Zealand.
Paul Gardner Engaging Scientists