Observatorio de I+D+i UPM

Memorias de investigación
Tesis:
FAIR approaches applied to unraveling Plant-Pathogen Interactions Data and RNA Processing Evolution
Año:2016
Áreas de investigación
  • Ciencias naturales y ciencias de la salud,
  • Ciencias de la computación y tecnología informática
Datos
Descripción
This thesis is the result of combining Semantic Web technologies (Ontology modeling/building), Data management (FAIR Principles) and exploration of biological data per se (plant-pathogen interactions / RNA Metabolism Evolution). The work and results of this thesis are divided on three main chapters. The first chapter (3.1) addresses the in silico evolutionary study we performed on the transcriptional and polyadenylation machineries in the fungal kingdom. Being both of them key processes involved the maturation of pre-mRNAs, we decided to analyze the complete ortholog/paralog network of the participant proteins, as well as whole- protein domain conservation studies. We found a significant number of proteins and domains not conserved among different taxonomic groups, with some proteins being exclusively present in some fungal clusters. Particularly, species belonging to the Microsporidia phylum present the lowest level of conservation. The second chapter (3.2) focuses on describing the complete modeling and construction of the Plant-Pathogen Interactions Ontology (PPIO), a formal ontological model that represents the entity-relationships that hold within the plant-pathogen knowledge domain. We based the PPIO modeling in grounded biological principles and recommended good practices in ontology building, and our intention is make it a core resource for reuse by the plant research community. In this chapter we also discuss the merge of the PPIO with the resulting ontology of chapter 3.3, as well as the steps taken to make the ontology fulfill the FAIR principles of data management and publication. The work described in the third chapter (3.3) deals with the transformation workflow of a relevant host-pathogen related database (PHI-base) and the datasets from chapter 3.1 to a form that firmly adheres to each of the FAIR Principles. The PHI-base-to-FAIR transformation work, called Semantic PHI-base, was published in the form of an article in the Frontiers in Plant Science Journal, being first public data repository designed to be fully compliant with the spirit of the FAIR data principles.
Internacional
Si
ISBN
Tipo de Tesis
Doctoral
Calificación
Sobresaliente cum laude
Fecha
Esta actividad pertenece a memorias de investigación
Participantes
  • Director: Mark Denis Wilkinson (UPM)
  • Autor: Alejandro Rodriguez Iglesias (UPM)
  • Director: Ane Sesma Galarraga (UPM)
Grupos de investigación, Departamentos, Centros e Institutos de I+D+i relacionados
  • Creador: Grupo de Investigación: BIOLOGÍA MOLECULAR Y COMPUTACIONAL
  • Centro o Instituto I+D+i: Centro de Biotecnología y Genómica de Plantas, CBGP
  • Departamento: Biotecnología - Biología Vegetal
S2i 2022 Observatorio de investigación @ UPM con la colaboración del Consejo Social UPM
Cofinanciación del MINECO en el marco del Programa INNCIDE 2011 (OTR-2011-0236)
Cofinanciación del MINECO en el marco del Programa INNPACTO (IPT-020000-2010-22)