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

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


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.


  • Gene Ontology
  • Factor Graph
  • Automatic function prediction

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Correspondence to F. Spetale .

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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.

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  • Print ISBN: 978-981-10-4085-6

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