Project repository for the NSF-funded project Enabling Machine-actionable Semantics for Comparative Analysis of Trait Evolution.The overall objective of the project is to create infrastructure that will provide comparative trait analysis tools easy access to algorithms powered by machine reasoning with the semantics of trait descriptions. Work is centered on the following specific aims lead by project personnel:
• Aim 1.1 - Generalizing ontotrace (without tree for missing data) (Hilmar, Jim, Wasila, Paula)
• Aim 1.2 - Semantic similarity and trait evolution (Sergei)
• Aim 1.3 - Quantitative properties of characters, states, and phenotypes using analysis of KB (Hilmar, Paula, Wasila)
• Aim 2.1 - Dirichlet Process Priors/HMM methods (Sergei, Josef)
• Aim 2.2 - Application of DPP/HMM to miniaturization (Wasila, Paula)
• Aim 3.1 - Ancestral state reconstruction simulations with ontological permutations (Todd, Sergei)
• Aim 3.2 - RPhenoscate package with ASR and structured Markov Models incorporating anatomical dependencies (Sergei, Josef)