sergeitarasov
commented
6 years ago I am particularly interested to work on some simple ontology-based model that will be able to simulate "real" morpho-characters. By this, I mean that if now we simulate character evolution over phylogenetic tree our output (i.e. characters) are just "0"s and "1"s. We can use ontologies to generate not "meaningless" numbers but "real" character statements and states with biological meaning and probably more realistic evolutionary mechanism.
I'd like to work on using the KnowledgeBase's API to query a set of traits and return an ontology that can then be used to build discrete character models (as in Sergei Tarasov's recent preprint) and to work on other phylogenetic comparative methods that can digest ontologies in useful and interesting ways to improve the modeling of trait evolution. I'd like to see what we can do to connect the output of the rphenoscape package to existing comparative methods packages in the R ecosystem.