Abstract
The protein sequence analysis can deal with various approaches in order to find the phenotypic and functional characteristics of the gene structure. Fortunately there are many models of genes already described in database with biological information.
Linking coffee gene annotations transcriptome to centralized biology information systems as Bio2RDF, offers the possibility of finding associated transcriptome relationships between them and between terms and concepts defined by semantic rules defined by ontologies.
Sesame was used as a repository to store information related triplets with coffee and transcriptomes index obtained from the Protein Data Bank (PDB), these relationships are the foundation for semantic search using SPARQL.
Data from the functional relationships searches are deployed through the endpoint provided by the repository from Sesame and Pubby.
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References
Hartwick, E.: The Cultural Turn in Geography: A New Link in the Commodity Chain. In: Encounters and Engagements between Economic and Cultural Geography. GeoJournal Library, vol. 104, pp. 39–46 (2012)
Li, W., Feng, J., Jiang, T.: Workshop: Transcriptome assembly from RNA-Seq data: Objectives, algorithms and challenges. In: IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), p. 271 (2011)
Castillo, L.F., Galeano, N., Isaza, G.A., Gaitan, A.: Construction of coffee transcriptoma networks base don gene annotation semantics. Journal of Integrative Bioinformatics, 1–13 (2012)
Coulet, A., Shan, N.H., Garten, Y., Musen, M., Altman, R.B.: Using text to build semantic networks for pharmacogenomics. J. Biomed. Inform. 43(6), 1009–1019 (2010)
Heath, T., Bizer, C.: Linked Data: Evolving the web into global Data Space. Morgan & Claypool Publishers series (2011)
Belleau, F., Nolin, M.-A., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics 41, 706–716 (2008)
Broekstra, J., Kampman, A., Van Harmelen, F.: Sesame: An Arquitecture for Storing and Querying RDF Data and Schema Information. Spinning the Semantic Web, 197–221 (2005)
DuCharme, B.: Learning SPARQL: Quering and Updating with SPARQL 1.1 (2011)
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© 2013 Springer International Publishing Switzerland
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Bertel-Paternina, L., Castillo, L.F., Gaitán-Bustamente, A., Galeano-Vanegas, N., Isaza, G. (2013). Search Functional Annotations Genetic Relationships of Coffee through Bio2RDF. In: Mohamad, M., Nanni, L., Rocha, M., Fdez-Riverola, F. (eds) 7th International Conference on Practical Applications of Computational Biology & Bioinformatics. Advances in Intelligent Systems and Computing, vol 222. Springer, Heidelberg. https://doi.org/10.1007/978-3-319-00578-2_7
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DOI: https://doi.org/10.1007/978-3-319-00578-2_7
Publisher Name: Springer, Heidelberg
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