PhylOnt: A domain-specific ontology for phylogeny analysis

Phylogenetic analyses can resolve historical relationships among genes, organisms or higher taxa. Understanding such relationships can elucidate a wide range of biological phenomena including the role of adaptation as a driver of diversification, the importance of gene and genome duplications in the evolution gene function, or the evolutionary consequences of biogeographic shifts. The variety of methods of analysis and data types typically employed in phylogenetic analyses can pose challenges for semantic reasoning due to significant representational and computational complexity. These challenges could be ameliorated with the development of an ontology designed to capture and organize the variety of concepts used to describe phylogenetic data, methods of analysis and the results of phylogenetic analyses. In this paper, we discuss the development of PhylOnt — an ontology for phylogenetic analyses, which establishes a foundation for semantics-based workflows including meta-analyses of phylogentic data and trees. PhylOnt is an extensible ontology, which describes the methods employed to estimate trees given a data matrix, models and programs used for phylogenetic analysis and descriptions of phylogenetic trees including branch-length information and support values. The relational vocabulary included in PhylOnt will facilitate the integration of heterogeneous data types derived from both structured and unstructured sources. To illustrate the utility of PhylOnt, we annotated scientific literature to support semantic search. The semantic annotations can subsequently support workflows that requiring the exchange and integration of heterogeneous phylogenetic information.