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BioGateway: a semantic systems biology tool for the life sciences

(2009) BMC BIOINFORMATICS. 10(suppl. 10).
Author
Organization
Abstract
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. Access to the system and supplementary information (such as a listing of the data sources in RDF, and sample queries) can be found at http://www.semantic-systems-biology.org/biogateway.
Keywords
DATABASE, STANDARDS, KNOWLEDGE, GENE ONTOLOGY, WEB TECHNOLOGIES, BIOMEDICAL ONTOLOGIES, INFORMATION-RETRIEVAL, DATA INTEGRATION, UNIPROT, ANNOTATION

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Citation

Please use this url to cite or link to this publication:

MLA
Antezana San Roman, Erick Zimar et al. “BioGateway: a Semantic Systems Biology Tool for the Life Sciences.” BMC BIOINFORMATICS 10.suppl. 10 (2009): n. pag. Print.
APA
Antezana San Roman, E. Z., Blondé, W., Egana, M., Rutherford, A., Stevens, R., De Baets, B., Mironov, V., et al. (2009). BioGateway: a semantic systems biology tool for the life sciences. BMC BIOINFORMATICS, 10(suppl. 10).
Chicago author-date
Antezana San Roman, Erick Zimar, Ward Blondé, Mikel Egana, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, and Martin Kuiper. 2009. “BioGateway: a Semantic Systems Biology Tool for the Life Sciences.” Bmc Bioinformatics 10 (suppl. 10).
Chicago author-date (all authors)
Antezana San Roman, Erick Zimar, Ward Blondé, Mikel Egana, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, and Martin Kuiper. 2009. “BioGateway: a Semantic Systems Biology Tool for the Life Sciences.” Bmc Bioinformatics 10 (suppl. 10).
Vancouver
1.
Antezana San Roman EZ, Blondé W, Egana M, Rutherford A, Stevens R, De Baets B, et al. BioGateway: a semantic systems biology tool for the life sciences. BMC BIOINFORMATICS. 2009;10(suppl. 10).
IEEE
[1]
E. Z. Antezana San Roman et al., “BioGateway: a semantic systems biology tool for the life sciences,” BMC BIOINFORMATICS, vol. 10, no. suppl. 10, 2009.
@article{783852,
  abstract     = {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.
Access to the system and supplementary information (such as a listing of the data sources in RDF, and sample queries) can be found at http://www.semantic-systems-biology.org/biogateway.},
  articleno    = {S11},
  author       = {Antezana San Roman, Erick Zimar and Blondé, Ward and Egana, Mikel and Rutherford, Alistair and Stevens, Robert and De Baets, Bernard and Mironov, Vladimir and Kuiper, Martin},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keywords     = {DATABASE,STANDARDS,KNOWLEDGE,GENE ONTOLOGY,WEB TECHNOLOGIES,BIOMEDICAL ONTOLOGIES,INFORMATION-RETRIEVAL,DATA INTEGRATION,UNIPROT,ANNOTATION},
  language     = {eng},
  number       = {suppl. 10},
  pages        = {15},
  title        = {BioGateway: a semantic systems biology tool for the life sciences},
  url          = {http://dx.doi.org/10.1186/1471-2105-10-S10-S11},
  volume       = {10},
  year         = {2009},
}

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