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Linking Genome Annotation Projects with Genetic Disorders using Ontologies

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Abstract

Genome sequencing projects generate vast amounts of data of a wide variety of types and complexities, and at a growing pace. Traditionally, the annotation of such sequences was difficult to share with other researchers. Despite the fact that this has improved with the development and application of biological ontologies, such annotation efforts remain isolated since the amount of information that can be used from other annotation projects is limited. In addition to this, they do not benefit from the translational information available for the genomic sequences. In this paper, we describe a system that supports genome annotation processes by providing useful information about orthologous genes and the genetic disorders which can be associated with a gene identified in a sequence. The seamless integration of such data will be facilitated by an ontological infrastructure which, following best practices in ontology engineering, will reuse existing biological ontologies like Sequence Ontology or Ontological Gene Orthology.

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Notes

  1. http://www.obofoundry.org/cgi-bin/detail.cgi?id=evidencecode

References

  1. Stein, L., Genome annotation: From sequence to biology, Nat. Rev. Genet. 2(7):493–503, 2001.

    Article  Google Scholar 

  2. Eilbeck, K., Lewis, S., Mungall, C., Yandell, M., Stein, L., Durbin, R., and Ashburner, M., The sequence ontology: A tool for the unification of genome annotations. Genome Biol. 6(5):R44, 2005.

    Article  Google Scholar 

  3. Moore, B., Fan, G., and Eilbeck, K., SOBA: Sequence ontology bioinformatics analysis. Nucleic Acids Res. 38(5):W161–W164, 2010.

    Article  Google Scholar 

  4. Holt, C., and Yandell, M., MAKER2: An annotation pipeline and genome-database management tool, for second-generation genome projects. BMC Bioinformatics 12(1):491–505, 2011.

    Article  Google Scholar 

  5. The Gene Ontology Consortium: Gene ontology: Tool for the unification of biology. Nat. Genet. 25:25–29, 2000.

    Google Scholar 

  6. Turner, F., Clutterbuck, D., and Semple, C., Pocus: Mining genomic sequence annotation to predict disease genes. Genome Biol. 4(R75), 2003.

  7. Mott, R., Annotation, genetics and transcriptomics. Modern Genome Annotation, pp. 123–138. Springer Verlag, 2008.

  8. Osborne, J., Flatow, J., Holko, M., Lin, S., Kibbe, W., Zhu, L., Danila, M., Feng, G., and Chisholm, R., Annotating the human genome with disease ontology. BMC Genomics 10(Suppl 1):S6, 2009.

    Article  Google Scholar 

  9. Miñarro Gimenez, J.A., Madrid, M., and Fernandez-Breis, J.T., OGO: An ontological approach for integrating knowledge about orthology. BMC Bioinformatics 10(Suppl 10):S13, 2009.

    Article  Google Scholar 

  10. The Quest for Orthologous Consortium, http://questfororthologs.org/ (Last accessed: October 2012).

  11. Dessimoz, C., Gabaldón, T., Roos, D.S., Sonnhammer, E.L.L., and Herrero, J., The Quest for Orthologs Consortium: Toward community standards in the quest for orthologs. Bioinformatics 28(6):900–904, 2012.

    Article  Google Scholar 

  12. Schmitt, T., Messina, D.N., Schreiber, F., and Sonnhammer, E.L., Letter to the editor: Seqxml and orthoxml: Standards for sequence and, orthology information. Brief. Bioinform. 12(5):485–488, 2011.

    Article  Google Scholar 

  13. Wu, F., Mueller, L., Crouzillat, D., Petiard, V., and Tanksley, S., Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the Euasterid Plant Clade. Genetics 174(3):1407–1420, 2006.

    Article  Google Scholar 

  14. Antezana, E., Egaña, M., Blondé, W., Illarramendi, A., Bilbao, I.N., De Baets, B., Stevens, R., Mironov, V., and Kuiper, M., The cell cycle ontology: An application ontology for the representation and integrated analysis of the cell cycle process. Genome Biol. 10(5):R58, 2009.

    Article  Google Scholar 

  15. Harvey, K., Pfleger, C., and Hariharan, I., The drosophila mst ortholog, hippo, restricts growth and cell proliferation and promotes apoptosis. Cell 114:457–467, 2003.

    Article  Google Scholar 

  16. Miñarro-Giménez, J., Egaña Aranguren, M., Martínez-Béjar, R., Fernández-Breis, J., and Madrid, M., Semantic integration of information about orthologs and diseases: The ogo system. Journal of Biomedical Informatics 44:1020–1031, 2011.

    Article  Google Scholar 

  17. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., and Apweiler, R., The Gene Ontology Annotation (GOA) database: Sharing knowledge in Uniprot with gene ontology. Nucleic Acids Res. 32:D262–D266, 2004.

    Article  Google Scholar 

  18. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Federhen, S., et al., Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39(suppl 1):D38–D51, 2011.

    Google Scholar 

  19. Smith, B., Ceusters, W., Klagges, B., Kohler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A., and Rosse, C., Relations in biomedical ontologies. Genome Biol. 6(R46), 2005.

  20. Bard, J., Rhee, S., and Ashburner, M., An ontology for cell types. Genome Biol. 6:21–26, 2005.

    Article  Google Scholar 

  21. Robinson, P., Khler, S., Bauer, S., Seelow, D., Horn, D., and Mundlos, S., The human phenotype ontology: A tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet. 83:610–615, 2008.

    Article  Google Scholar 

  22. Tatusov, R., Fedorova, N., Jackson, J., Jacobs, A., Kiryutin, B., Koonin, E., Krylov, D., Mazumder, R., Mekhedov, S., Nikolskaya, A., Rao, S., Smirnov, S., Sverdlov, A., Vasudevan, S., Wolf, Y., Yin, J., and Natale, D., The cog database: An updated version includes eukaryotes. BMC Bioinformatics 4:41–55, 2003.

    Article  Google Scholar 

  23. Nagaraj, S.H., Gasser, R.B., and Ranganathan, S., A hitchhiker’s guide to expressed sequence tag (EST) analysis. Brief. Bioinform. 8(1):6–21, 2007.

    Article  Google Scholar 

  24. Egaña Aranguren, M., Stevens, R., Antezana, E., Fernández-Breis, J., Kuiper, M., and Mironov, V., Technologies and best practices for building bio-ontologies. In: Knowledge-based bioinformatics: From analysis to interpretation, pp. 68–86. Wiley, 2010.

  25. Bizer, C., Heath, T., and Berners-Lee, T., Linked data - The story so far. International Journal on Semantic Web and Information Systems 5(3):1–22, 2009.

    Article  Google Scholar 

  26. Miñarro-Giménez, J.A., Egaña Aranguren, M., Villazón-Terrazas, B., and Fernández-Breis, J.T., Publishing orthology and diseases information in the linked open data cloud. Current Bioinformatics 7(3):255–266, 2012. doi:10.2174/157489312802460811.

    Article  Google Scholar 

  27. Identifiers.org, http://identifiers.org/. Last accessed: October 2012

  28. Miñarro Gimenez, J., Egaña Aranguren, M., Garcia-Sanchez, F., and Fernández-Breis, J., A semantic query interface for the ogo platform. Lect. Notes Comput. Sci. 6266:128–142, 2010.

    Article  Google Scholar 

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Acknowledgements

This project has been possible thanks to the funding of the Spanish Ministry of Science and Innovation through grant TIN2010-21388-C02-02 and cofunded by the FEDER Programme. M.C. Legaz-García is supported by the Fundación Séneca through fellowship 15555/FPI/2010. M. Madrid is supported by the Spanish Ministry of Science and Innovation through fellowship JCI-2010-07513.

Conflict of interest  The authors declare that they have no conflict of interest.

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Correspondence to Jesualdo Tomás Fernández-Breis.

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Legaz-García, M., Miñarro-Giménez, J.A., Madrid, M. et al. Linking Genome Annotation Projects with Genetic Disorders using Ontologies. J Med Syst 36 (Suppl 1), 11–23 (2012). https://doi.org/10.1007/s10916-012-9890-7

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