BOWiki

Recent biological research has generated an increasing amount ofdata, resulting in a complex assemblage of information.While sequence analysis and micro-array experiments have revealed informationabout genes, these might not have been intensively studied or even remain unknown.To assist the biological community with gathering and structuringtheir knowledge, a software projectnamed "BOWiki" has been developed. Its application can make biological knowledgeeasier to handle for both humans and computers.

BOWiki is a Semantic Wiki for collaborative editing ofbiomedical ontologies and gene data. By applying the [http://onto.eva.mpg.de/publication/2006/BHLVKH06/ Ontology of Functions] ,it provides the functionality for editing of gene functions and annotations. The BOWiki is capable of using a type system based on an OWL ontology together with a description logic reasoner in order to perform consistency checks and queries.

Background

BOWiki has been developed for two main reasons: first, it is to be used for collaborative knowledge acquisition and ontology curation for a newly developed biomedical ontology, the Ontology of Functions (); second, it was developed as a response to a letter in the journal Nature calling for a "gene function wiki" (http://www.nature.com/nature/journal/v439/n7076/full/439534a.html).

Therefore, BOWiki allows the manipulation, creation and curation of biomedical ontologies, in particular the Ontology of Functions, and the annotation of gene data using the Ontology of Functions and other ontologies such as the Gene Ontology.

BOWiki augments Semantic MediaWiki with relations having more than 2 arguments

BOWiki modifies the Semantic MediaWiki in that it enables relations with more than two arguments to be written in the wiki pages. The standard releases of Semantic MediaWiki does not allow this, and neither do most other semantic wikis. Instead, such relations must be coded indirectly, using techniques such as those recommended in the World Wide Web Consortium paper [http://www.w3.org/TR/swbp-n-aryRelations/ "Defining N-ary Relations on the Semantic Web"] .

An example of a four place relation in BOWiki is the following function ascription (assumed to appear on the "MAL21" wiki page (describing the sugar transporting protein MAL21):

with the intended meaning that the protein MAL21 realizes the function "sugar transporter activity" (taken from the Gene Ontology) by means of a process "sugar transport" (taken from the Gene Ontology) in the context of a human body.

Using the Ontology of Functions

The biomedical knowledge held in BOWiki is described using the Ontology of Functions, which is embedded in a biomedical core ontology based on the General Formal Ontology. The word "function" here is used in the sense that the function of the heart is to pump blood.

To quote [4] : "The Ontology of Functions (OF) is based on the assumption that functions can be specified using requirements and a goal. An entity, e.g. a gene product, plays the role specified in the function – it has the function. A biological process is, in turn, the realization of the described function". Further explanation can be found in the presentation [http://leechuck.de/talks/ismb.pdf "A top-level ontology of functions and its application in the Open Biomedical Ontologies"] .

References

* [1] [http://bowiki.net BOWiki main page] . URL last accessed November 22, 2007.
* [2] [http://leechuck.de/talks/ismb.pdf "A top-level ontology of functions and its application in the Open Biomedical Ontologies"] , by Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, and Janet Kelso. Presentation to the Conference on Intelligent Systems for Molecular Biology, 2006. URL last accessed September 27, 2006.
* [3] [http://www.w3.org/TR/swbp-n-aryRelations/ "Defining N-ary Relations on the Semantic Web"] , by Pat Hayes and Chris Welty, edited by Natasha Noy and Alan Rector, W3C Working Group Note 12 April 2006. URL last accessed September 27, 2006.
* [4] http://bio-ontologies.man.ac.uk/download/HoehndorfEtAlWiki.pdf "The design of a wiki-based curation system for the Ontology of Functions"] by Robert Hoehndorf, Kay Prüfer, Michael Backhaus, Johann Visagie, and Janet Kelso. URL last accessed September 27, 2006.
* [5] [http://www2007.org/workshops/paper_46.pdf www2007 conference paper]