1. Best of both worlds :
Combining the user-friendliness of Wikis and
the rigor of biological databases
Sylvain Brohée
Roland Barriot
Yves Moreau

2. 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)

3. 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.

4. 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, …).

5. Classical wiki representation
Wiki database
(PostgreSQL, MySQL)
Administration
Wiki
User rights
User preferences MediaWiki
Wiki configuration (PHP)
website
Images
Articles
Stats
History
…
ext 1 ext 2

6. 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.

7. Wiki with WikiOpener extension
Wiki database
Administration
User rights
Wiki configuration MediaWiki
Wiki
Image Articles
(PHP)
website
s Data
Stats Layout
… Form fields
ext 2 ... Extensions
WikiOpener
WikiOpener components (PHP)
Web DAS Flat
Database ...
Other data sources
service track files

8. Applications
CHDWiki YTPdb
Congenital Heart Defects Yeast Transport Proteins
http://homes.esat.kuleuven.be/~bioisuer/chdwiki http://homes.esat.kuleuven.be/~sbrohee/ytpdb

9. A typical WikiOpener page

10. 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).
 Edition of structured data
 Non structured text from the
main database

11. WikiOpener forms

12. How does it work?
A simple Bibliography example

13. How does it work?
A simple Bibliography example
YTPdb
gene substrate
Wiki database Raw text of the Bibliography article
references
= References =
<wikiopener>getReferences|Refer ...
Administration encesLayout|All </wikiopener>
User rights
Wiki configuration
WikiOpener component getReference.p
Articles Returns an array of arrays.
... Raw text of the ReferenceLayout article
Bibliography References.foreach <?php
ReferenceLayout *{NAME}{TITLE}{YEAR}{JOURNAL} $result = array();
References.end_foreach ...
if (param[0] == “All”) {
$query = “SELECT * FROM
YTPDB.references”;}
...
return $result;
?>

14. 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

15. Thanks
 Roland Barriot
 Yves Moreau
 Bernard Thienpont
 Jeroen Breckpot
 Koen Devriendt
 Bruno André