Best of both worlds : Combining the user-friendliness of Wikis and

the rigor of biological databases

Sylvain Brohée

Roland Barriot

Yves Moreau

Biological databases

Databases are crucial in almost any biological research.

More and more biological databases (1170 described in NAR since 2004)

Large (Ensembl, pubmed, …)

Smaller and more specialized

Maintenance problem

abundant literature

funding comes to its end

curator leaves the lab

Solution : collaborative databases

Use of the MediaWiki engine (PHP)

MediaWiki advantages

More and more biological collaborative databases are based on the MediaWiki motor (Wikiprotein, WikiPathways, ...).

Free all-in-one solution to build collaborative databases :

(Almost) no programming skills needed.

User rights (read only, edition, …) managed.

User friendly and wide spread system.

+

MediaWiki drawbacks

All data are contained in one unique underlying database.

All pages have to be created and filled manually.

Data are not structured (free text).

Generally, biological databases are very well structured. Some consist only in a set of tables.

No possibility to include tools (blast, prioritization, …).

-

Classical wiki representation

MediaWiki(PHP)

Wikiwebsite

Wiki database(PostgreSQL, MySQL)

AdministrationUser rights

User preferencesWiki configuration

ImagesStats

…

ArticlesHistory

ext 1 ext 2

Mediawiki extensions

MediaWiki extensions are pieces of PHP code used to improve the existing wiki functionalities or to bring new ones.

We developed WikiOpener an extension to MediaWiki :

Easy (automated) inclusion and edition of external data

Include code in order to run tools

Automatic creation of wiki articles.

Wiki with WikiOpener extension

MediaWiki(PHP)

WikiOpenerext 2 ... Extensions

Wiki database

AdministrationUser rights

Wiki configuration

ArticlesData

LayoutForm fields

Image s

Stats…

...

Wikiwebsite

Other data sourcesDatabaseWeb

serviceFlat files

DAStrack

WikiOpener components (PHP)

Applications

CHDWiki

Congenital Heart Defectshttp://homes.esat.kuleuven.be/~bioisuer/chdwiki

YTPdb

Yeast Transport Proteinshttp://homes.esat.kuleuven.be/~sbrohee/ytpdb

A typical WikiOpener page

A typical WikiOpener page

Structured data coming from an external relational database.

Layout is specified as a wiki page.

Automatically displayed on all pages of type (namespace) Ytpdbgene (even if it is not manually created).

Non structured text from the main database

Edition of structured data

WikiOpener forms

How does it work? A simple Bibliography example

How does it work? A simple Bibliography example

Wiki database

AdministrationUser rights

Wiki configuration

Articles...

BibliographyReferenceLayout

= References =<wikiopener>getReferences|Refer encesLayout|All </wikiopener>

substrategene

referencesRaw text of the Bibliography article

References.foreach*{NAME}{TITLE}{YEAR}{JOURNAL}References.end_foreach

Raw text of the ReferenceLayout article

...

WikiOpener component getReference.pReturns an array of arrays.

<?php$result = array();...if (param[0] == “All”) {$query = “SELECT * FROM

YTPDB.references”;}...return $result;

?>

YTPdb

Conclusion

WikiOpener solves the main drawbacks of biological wikis

Display and edition of both formatted and unformatted text.

Displayed data may come come from everywhere (database, DAS track, web service).

Automatic creation of wiki pages filled with the external data.

Easy integration of code (javascript, PHP, ...) to run tools.

http://www.mediawiki.org/wiki/Extension:WikiOpener

Thanks

Roland Barriot

Yves Moreau

Bernard Thienpont

Jeroen Breckpot

Koen Devriendt

Bruno André