Linked biology
Eduardo Miranda · 2013
A large number of studies in biology, including those involving phylogenetic trees reconstruction, result in the production of a huge amount of data -e.g., phenotype descriptions, morphological data matrices, phylogenetic trees, etc. Biologists increasingly face a challenge and opportunity of effectively discovering useful knowledge crossing and comparing several pieces of information, not always linked and integrated.In this work, we are interested in a specific biology context, in which biologists apply computational tools to build and share digital descriptions of living beings.We propose a process that departs from fragmentary data sources, which we map to graphs, towards a full integration of descriptions through ontologies.Graph databases mediate this evolvement process.They are less schema dependent and, since an ontology is also a graph, the mapping process from the initial graph towards an ontology becomes a sequence of graph transformations.Our motivation stems from the idea that transforming phenotypical descriptions in a network of relationships and looking for links among related elements will enhance the ability of solving more complex problems supported by machines.This work details the design principles behind our process and two practical implementations as proof of concept.ix First and foremost, I would like to thank my parents, Elizabeth and José, who taught me the value of hard work and education and for the support and dedication throughout my life.My sisters, Mayara and Patrícia for their warmth over the years and for encouraging me to pursue my dreams.I also need to thank Patrícia for helping me to overcome my writing weakness and for correcting my papers.My grandparents, Carlos and Delizete for their wisdom and faith in me.My aunts, Elizete and Simone, my uncles Elizeu and Grei and my cousins, Nícolas and Thais for their continuous encouragement.My girlfriend, Ana Carolina for her support, encouragement and for being part of this journey, even when being at a distance.You experienced all of the ups and downs of