Towards a Linked Open Data Model for Coffee Functional Relationships
The development of technologies for massively disclose genetic information stored within cells generated the genomics revolution, where everyday exponentially growing databases with the description of the chemical structure of novel genes obtained with the automated nucleic acid sequencing. Each of these sequences is necessary to assign a function, in a process known as gene annotation comparing information of unknown sequence with sequences previously studied in the laboratory. This will identify candidate genes associated with traits of interest such as disease susceptibility or resistance, adaptation to the environment or animal or plant production. Given the volume of information, it is necessary that this be presented in a structured way so that such comparisons can be performed by computer agents quickly and it is open to the possibility of generating new knowledge by finding features and novel relationships between genes. This paper aims to present a bioinformatic application for functional relations search of transcriptome for coffee genetic material provided by the Coffee Investigation Center (CENICAFE), using the Bio2RDF biological database, applying new standards for LOD (Linked Open data) necessary to communicate effectively with other reference databases already operating under the scheme or Semantic Web.
Keywordsfunctional gene networks Semantic Web bioinformatics Linked Data Bio2RDF
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- 1.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)Google Scholar
- 2.Berners-Lee, T.: Semantic Web Road map (1998), http://www.w3.org/DesignIssues/Semantic.html (retrieved May 2012)
- 3.Linked Data-Connect Distributed Data across the web, http://linkeddata.org/
- 4.The Linking Open Data cloud diagram, http://lod-cloud.net/
- 7.Deus, H.F., Stanislaus, R., Veiga, D.F., Behrens, C., Wistuba II, Minna, J.D., Garner, H.R., Swisher, S.G., Roth, J.A., Correa, A.M., Broom, B., Coombes, K., Chang, A., Vogel, L.H., Almeida, J.S.: A Semantic Web management model for integrative biomedical informatics. 2008 Google Scholar
- 10.Chen, B., Ding, Y., Wang, H., Wild, D.J., Dong, X., Sun, Y., Zhu, Q., Sankaranarayanan, M.: Chem2Bio2RDF: A Linked Open Data Portal for Systems Chemical Biology. Web Intelligence, 232–239 (2010)Google Scholar
- 12.García-Godoy, M.J., Navas-Delgado, I., Aldana-Montes, J.: Bioqueries: a social community sharing experiences while querying biological linked data. Published in Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pp. 24–31. ACM, New York (2012) ISBN: 978-1-4503-1076-5Google Scholar
- 14.Gómez-Pérez, A., Fernández-López, M., Corcho, O.: Ontological engineering, Springer Verlag as part of the Advanced Information and Knowledge Processing series (2004) ISBN 1-85233-551-3 Google Scholar