Wikis at workA short introduction to 'wikis' and

wikis for biology

Dan Bolser and Paolo Romano

URL for slides: http://

Overview of today's course

Session 1 (35 min): What is a wiki? – A gentle introduction to the wiki

concept, and a look at Wikipedia.

Session 2 (35 min)

Biological wikis! – A review of some of the most important wikis for biology (BioWikis).

BREAK (15 min)

Overview of today's course

Session 3 (35 min)

Semantic MediaWiki – Software for 'data wikis'. Cell Lines Wiki – A pilot scientific wiki.

Practical session (60 min)

Editing Wikipedia (for the first time?) Working with Cell lines Wiki – A gentle introduction

to some of the key features.

Session 1

What is a wiki?

Wiki means QUICK!

Old way:

Wiki is a quicker way to let peopleput content on the web

Wiki is a quicker way to let peopleput content on the web

Old way:

Wiki is a quicker way to let peopleput content on the web

Old way:

Wiki is a quicker way to let peopleput content on the web

Old way:

Host

HTML editor

FTP software

Domain name

Wiki is a quicker way to let peopleput content on the web

Old way:

Wiki is a quicker way to let peopleput content on the web

Old way:

Wiki way:

Wiki means QUICK!

There is no longer one single 'point of control' for managing web content.

Content is managed by a decentralized community of participating users.

Wiki is radically different!

Is this good or bad?

Other advantages of wiki

There are many other advantages over 'traditional' web publishing...

Notification of changes History of changes Discussion of changes

The rise of the wiki

Condensed history

1994: Cunningham coined the term 'wiki'. A site (for software developers) with pages that can

be edited via the browser, each with a page history.

Over the next five years it spawned alternative wiki applications and websites (wiki culture).

By 2000, it had developed lots of of spin-off content, most notably MeatballWiki (for general discussion).

2001, Wikipedia launched.

2007, Wikipedia in the worlds top 10 web sites.

Wikipedia

Size Stats.

Growth Research.

Rules e.g. Deleting content.

Culture e.g. Anatomy of a talk page.

Almost all of its articles can be edited by anyone with access to the site, and it has about 90,000 regularly active contributors.

Wikipedia

Size 19.7 million articles

3.7 million in English 847,069 in Italian (4th out of 282)

2.7 billion monthly hits from the US alone.

7th most popular site in the world. The largest and most popular

general reference work.

Wikipedia

Growth (Kittur) Wikipedia has been

growing exponentially since 2002 (Voss)

“wisdom of crowds” or “elite users”

a large number of people with a small number of edits, or

a core group who do most of the work?

Wikipedia

Rules Their are no rules! The 'five pillars' of

Wikipedia' Standard deletion

procedure...

Wikipedia

Culture Their are no rules! The 'five pillars' of

Wikipedia' Discussion!

(Not bureaucracy)

Moving on...

Is WP, or something like it, the future for science?

Lets find out in Session 2!

Session 1, References

http://wikipedia.org/wiki/History_of_wikis

http://wikipedia.org/wiki/Wikipedia

1) Voss, J. Measuring Wikipedia. In Proceedings of the ISSI 2005 (Stockholm, Sweden, July 24-28, 2005).

2) Kittur A, Chi EH, Pendleton BA, Suh B, Mytkowicz T. Power of the few vs. wisdom of the crowd: Wikipedia and the rise of the bourgeoisie. CHI 2007.

http://wikipedia.org/wiki/Wikipedia:Five_pillars

http://meta.wikimedia.org/wiki/ Research:Newsletter/2011-07-25

Session 2

Scientific wikis

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Community annotation

32

Annotation

33

Annotation

34

Community annotation

Driven by two key factors:

The vast increase in biological data

The clear success of Wikipedia

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BioMoore's Law

Over time: Cost per unit of information can be decreased by

orders of magnitude. Throughput is increased by orders of magnitude.

Fan et al. 2006. Nat Rev Genet.

Comprehensive disease studies that might require ~1bn genotypes would now cost only a few million dollars. Revolution in human genetics.

36

BioMoore's Law

Over time: Cost per unit of information can be decreased by

orders of magnitude. Throughput is increased by orders of magnitude.

Fan et al. 2006. Nat Rev Genet.

Comprehensive disease studies that might require ~1bn genotypes would now cost only a few million dollars. Revolution in human genetics.

37

Community annotationis essential

Centralised databases can't cope with annotating the influx of data.

Less investment in more specialised data. Fewer people with a stake. Specialists more disparate.

Communities are smaller and more focused.

Do wikis hold the answer? Wikipedia as a model…

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But Wikipedia isn’t always the answer ...

• Wikipedia is an educational resource.

– All articles are encyclopaedic in style.

– Explicitly forbids data from ‘original research’:

• http://wikipedia.org/wiki/Wikipedia:No_original_research

– “Wikipedia does not publish original research”.

– No tools for the specific analysis, presentation, or collection of ‘biological’ data.

• BioWikis!

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BioWikis

Wikis with a biological subject matter, customized for analysis, presentation and collection of specific biological data and biological data types:

Wikis for biology

Proteopedia

http://proteopedia.org/

Aim – To make knowledge about proteins accessible.

Features: Interactive 3D viz. Contributions linked to

publications.

Problems Doesn't work on all

browsers. Can be slow.

Reference Hodis, E. et al., 2008. Proteopedia

- a scientific “wiki” bridging the rift between three-dimensional structure and function of biomacromolecules. Genome biology, 9(8), p.R121.

WikiPathways

http://wikipathways.org

Aim – The curation of biological pathways.

Features: Interactive pathway

editing. Integrated to many

biological databases.

Problems Doesn't work on all

browsers. Can be slow.

Reference Pico, A.R. et al., 2008.

WikiPathways: pathway editing for the people. PLoS biology, 6(7), p.e184.

EcoliWiki

http://ecoliwiki.net/

Aim – Share info related to non-pathogenic E. coli.

Features: Very extensive and

well structured domain information.

Referencing is good.

Problems Big resource Specific focus, could it

be applied to others?

Reference EcoliWiki, 2007. EcoliHub’s

subsystem for community annotation. http://ecoliwiki.net.

CHDWiki

http://goo.gl/info/Zxg8H

Aim(?) – Geneticists, clinicians, and mol. biologists working on Congenital Heart Defects.

Features: Curated gene lists. PPI browser.

Problems Very old MediaWiki

fork Used?

Reference Barriot, R. et al., 2010.

Collaboratively charting the gene-to-phenotype network of human congenital heart defects. Genome medicine, 2(3), p.16.

SEQwiki

http://seqwiki.org

Aim – a catalogue of analysis tools and, technologies for NGS.

Features Structured data. Linked to an

established forum.

Problems Data can become

error prone. Data is difficult to

centrally manage.

Reference Li J.W., et. al. 2012. The

SEQanswers wiki: A wiki database of tools for high throughput sequencing analysis. Nucleic Acids Research 2012 Database special issue.

Listing of biowikis...

http://bioinformatics.org/wiki/BioWiki

BioWikis

There is a variety of different systems.

All seek to 'recognize' contributors (biologists) in a way more familiar to scientists than Wikipedia.

Most have features not found in Wikipedia. Some projects use the base of Wikipedia to

successfully build integrated 'sub-projects'...

The MCB Portal in Wikipedia

http://en.wikipedia.org/wiki/Wikipedia:MCB

Aim – Better organize information related to molecular and cell biology on Wikipedia.

Features Integrated with WP

Problems The project can be

confusing to those unfamiliar with Wikipedia.

Reference ...

Gene Wiki

http://en.wikipedia.org/wiki/Portal:Gene_Wiki

Aim – applying community intelligence to gene annotation.

Special features: Semi-automatic gene

curation system.

Problems The project can be

confusing to those unfamiliar with Wikipedia.

Reference Huss, J.W. et al., 2008. A gene

wiki for community annotation of gene function. PLoS biology, 6(7), p.e175.

Wikis for Cancer?

Some aditional references

1. Fan JB, Chee MS, Gunderson KL. Highly parallel genomic assays. Nature reviews. Genetics 7, 632-44 (2006).

2. The Molecular modelling blog post http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/

1. http://bifx.org/wiki/BioWiki2. Daub, J. et al., 2008. The RNA WikiProject: community annotation of RNA families. RNA

(New York, N.Y.), 14(12), pp.2462-4. 3. Stehr, H. et al., 2010. PDBWiki: added value through community annotation of the Protein

Data Bank. Database, p.baq009-baq009.4. Flórez, L.A. et al., 2009. A community-curated consensual annotation that is continuously

updated: the Bacillus subtilis centred wiki SubtiWiki. Database : the journal of biological databases and curation, p.bap012

Session 3

Semantic MediaWiki

Semantic MediaWiki(a data wiki engine)

What is SMW?

Motivation

Frontend What you see as a

user of SMW.

Backend What you do as a

SMW site developer...

Data

Properties and types

Classes

Templates

Forms

Queries

References

SMW Homepage: http://semantic-mediawiki.org

MW Templates: http://www.mediawiki.org/wiki/Help:Templates

SF Homepage: http://www.mediawiki.org/wiki/ Extension:Semantic_Forms

SMW #ask: http://semantic-mediawiki.org/wiki/ Help:Inline_queries

SMW demo sites:

http://pgscdemo.referata.com

http://discoursedb.org

http://sandbox.referata.com

Cell Lines Wiki