Transforming a biological database withcollaboration

Paul Gardner

June 28, 2013

Paul Gardner Engaging Scientists: eResearch 2013

Today I will be presenting...

I How I inherited a sad and tired biological database

I and transformed it with collaborative editing

I and engaged a community by using Wikipedia.

Paul Gardner Engaging Scientists: eResearch 2013

What is RNA?

I RNA is a fundamental biological molecule, essential for untoldbiological processes

I New technologies are accelerating the rate of RNA discovery.I My aim is to build an analog to the Periodic Table for

classifying RNA families and motifs, enabling researchers topredict function.

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Paul Gardner Engaging Scientists: eResearch 2013

What is Rfam?

I A database of ncRNA alignments and structures

I Used for annotating RNAs in genome sequences, bioinformaticalgorithm development and molecular evolutionary analyses

Gardner et al. (2008) Rfam: updates to the RNA families databaseNucleic Acids Research.

Paul Gardner Engaging Scientists: eResearch 2013

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: eResearch 2013

This Wikipedia thing looks pretty good!

Paul Gardner Engaging Scientists: eResearch 2013

WikiProject RNA

I The WikiProjects are social corners of Wikipedia for interestedparties to discuss themed articles

I Involved in reviewing, ranking and rating articlesI Now rolled into the larger WikiProject Molecular and Cellular

Biology

Paul Gardner Engaging Scientists: eResearch 2013

How has the Wikipedia experiment gone?

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Year

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9089

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Total edits

Vandalism

Gardner et al. (2011) Rfam: Wikipedia, clans and the “decimal”release Nucleic Acids Research.

Paul Gardner Engaging Scientists: eResearch 2013

Who are these Wikipedians donating their time?

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Paul Gardner Engaging Scientists: eResearch 2013

What incentives can we give to Academics?

I Academics love publishing articles

I Introducing the “families track” at RNA Biology (IF:4.841)

I Publication requirements are an alignment & a Wikipediaarticle

I 100s of new families have been added thanks to this track

Paul Gardner Engaging Scientists: eResearch 2013

The pros and cons of presenting biological informationwithin Wikipedia

I Private Wiki or Wikipedia?I Wikipedia: pros - high profile, lots of editors, top Google hit, ...I Wikipedia: cons - need to follow ”rules”, article granularity,

vandalism, ...I Private Wiki: pros - granular as you like, your own rules

(invitation only vs public), ...I Private Wiki: cons - small communities (no Daniel Ramskold),

policing, maintenance, ...

I Eleven new Wiki-based databased were published in the lastdatabases issue of Nucleic Acids Research. Including:

I Directly incorporating Wikipedia: GeneWiki, Pfam, ...I Presenting information via Wikis: EcoliWiki, SNPedia &

WikiPathways, ...

Finn, Gardner, Bateman (2012) Making your database availablethrough Wikipedia: the pros and cons Nucleic Acids Research.

Paul Gardner Engaging Scientists: eResearch 2013

Wikipedia need you!

I What is the highest impact contribution academics can make?

I Rule 1: Register an AccountI Rule 2: Learn the Five Pillars

I ENCYC, NPOV, FREE, RESPECT, NORULES

I Rule 3: Be Bold, but Not Reckless

I Rule 4: Know Your Audience

I Rule 5: Do Not Infringe Copyright

I ...

Paul Gardner Engaging Scientists: eResearch 2013

Who might be reading about your field?

Paul Gardner Engaging Scientists: eResearch 2013

Thanks!

I The Rfam Consortium

I Wikipedians & the longtail!

PPG is supported by a Rutherford Discovery Fellowship from Government funding, administered by the RoyalSociety of New Zealand.

Paul Gardner Engaging Scientists: eResearch 2013