Formalising ylogenetic eriments: Ontologies and cal ference

The ontology of scientific experiments EXPO formalises the generic concepts of experimental design, methodology, and results representation. We describe an application of EXPO to describe phylogenetic experiments, focusing on a case study involving Solonedons. We explain how the details of the experiment were formalised using EXPO We argue that abductive inference is the basis of evolutionary phylogenetics, that inductive inference is necessary to generalise phylogenetic conclusions from sequences to genomes, and that deductive inference is also often required. This is novel because phylogenetic experiments are generally thought to be based on purely probabilistic methods. The recognition that different forms of logical inferences are taking place may enable novel techniques from logic to be applied.