BioGateway: A Semantic Systems Biology Tool for the Life Sciences
Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin
Journal article, Peer reviewed
Permanent lenke
http://hdl.handle.net/11250/2384279Utgivelsesdato
2009Metadata
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- Institutt for biologi [2614]
- Publikasjoner fra CRIStin - NTNU [38525]
Sammendrag
Background: Life scientists need help in coping with the plethora of fast growing and scattered
knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to
pose complex questions that address the properties of biological systems, independently from the
origin of the knowledge. Semantic Web technologies prove to be well suited for knowledge
integration, knowledge production (hypothesis formulation), knowledge querying and knowledge
maintenance.
Results: We implemented a semantically integrated resource named BioGateway, comprising the
entire set of the OBO foundry candidate ontologies, the GO annotation files, the SWISS-PROT
protein set, the NCBI taxonomy and several in-house ontologies. BioGateway provides a single
entry point to query these resources through SPARQL. It constitutes a key component for a
Semantic Systems Biology approach to generate new hypotheses concerning systems properties. In
the course of developing BioGateway, we faced challenges that are common to other projects that
involve large datasets in diverse representations. We present a detailed analysis of the obstacles
that had to be overcome in creating BioGateway. We demonstrate the potential of a
comprehensive application of Semantic Web technologies to global biomedical data.
Conclusion: The time is ripe for launching a community effort aimed at a wider acceptance and
application of Semantic Web technologies in the life sciences. We call for the creation of a forum
that strives to implement a truly semantic life science foundation for Semantic Systems Biology.