Building a biomedical semantic network in Wikipedia with Semantic Wiki Links

• Published in: Database : the journal of biological databases and curation Vol. 2012; p. bar060
• Main Authors: Good, Benjamin M, Clarke, Erik L, Loguercio, Salvatore, Su, Andrew I
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 2012
• Subjects: Biomedical Research; Databases, Genetic; Humans; Internet; Molecular Sequence Annotation; Original; Semantics
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/bar060

Wikipedia is increasingly used as a platform for collaborative data curation, but its current technical implementation has significant limitations that hinder its use in biocuration applications. Specifically, while editors can easily link between two articles in Wikipedia to indicate a relationship, there is no way to indicate the nature of that relationship in a way that is computationally accessible to the system or to external developers. For example, in addition to noting a relationship between a gene and a disease, it would be useful to differentiate the cases where genetic mutation or altered expression causes the disease. Here, we introduce a straightforward method that allows Wikipedia editors to embed computable semantic relations directly in the context of current Wikipedia articles. In addition, we demonstrate two novel applications enabled by the presence of these new relationships. The first is a dynamically generated information box that can be rendered on all semantically enhanced Wikipedia articles. The second is a prototype gene annotation system that draws its content from the gene-centric articles on Wikipedia and exposes the new semantic relationships to enable previously impossible, user-defined queries. DATABASE URL: http://en.wikipedia.org/wiki/Portal:Gene_Wiki.