OntoAvida: ontology for Avida digital evolution platform

OntoAvida develops an integrated vocabulary for the description of the most widely-used computational approach for studying evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).

The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of Avida, the most widely used computational approach for performing experimental evolution. The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. In addition, OntoAvida will allow researchers to make inference (e.g., on phenotypic plasticity) based on certain rules and constraints, facilitate the reproducibility of the in silico evolution experiments reported in the scientific literature, and trace the provenance of the data stored in AvidaDB, a semantic database that stores genomes and transcriptomes of more than a million digital organisms.