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Formalization of Gene Ontology relationships with factor graph towards Biological Process prediction

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Book cover VII Latin American Congress on Biomedical Engineering CLAIB 2016, Bucaramanga, Santander, Colombia, October 26th -28th, 2016

Part of the book series: IFMBE Proceedings ((IFMBE,volume 60))

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Abstract

Gene Ontology is a hierarchical controlled vocabulary for protein annotation. Its synergy with automatic classification methods, ensemble, has been widely used for the prediction of protein functions. Current classification methods use only the relation is_a and a few little part_of to generate prediction model. In this work we formalize the GO part_of, regulates; negatively_regulates and positively_regulates relationships through predicate logic. This formalization is incorporated within an ensemble method based on graph factor called Factor Graph GO Annotation. The proposed model is validated against four model organisms for GO Biological Process prediction.

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Authors and Affiliations

  1. CIFASIS-Conicet Institute, Bv. 27 de Febrero 210 Bis, Rosario, Argentina

    F. Spetale, P. Bulacio, F. Krsticevic & E. Tapia

  2. Facultad Regional San Nicolás, Universidad Tecnolgica Nacional, Colón 332, Buenos Aires, Argentina

    S. Ponce

Authors
  1. F. Spetale
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  2. P. Bulacio
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  3. F. Krsticevic
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  4. S. Ponce
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  5. E. Tapia
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Corresponding author

Correspondence to F. Spetale .

Editor information

Editors and Affiliations

  1. Asociación Colombiana de Bioingeniería y Electrónica Médica - ABIOIN, Bucamaranga, Colombia

    Isnardo Torres

  2. Universidad Pontificia Bolivariana - UPB, Centro de Bioingeniería, Medellín, Colombia

    John Bustamante

  3. Universidad Industrial de Santander, Escuela de Ing. Eléctrica, Electrónica, Bucaramanga, Colombia

    Daniel A. Sierra

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Spetale, F., Bulacio, P., Krsticevic, F., Ponce, S., Tapia, E. (2017). Formalization of Gene Ontology relationships with factor graph towards Biological Process prediction. In: Torres, I., Bustamante, J., Sierra, D. (eds) VII Latin American Congress on Biomedical Engineering CLAIB 2016, Bucaramanga, Santander, Colombia, October 26th -28th, 2016. IFMBE Proceedings, vol 60. Springer, Singapore. https://doi.org/10.1007/978-981-10-4086-3_15

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  • DOI: https://doi.org/10.1007/978-981-10-4086-3_15

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-10-4085-6

  • Online ISBN: 978-981-10-4086-3

  • eBook Packages: EngineeringEngineering (R0)

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