Ontology for the Avida digital evolution platform

Sci Data. 2023 Sep 9;10(1):608. doi: 10.1038/s41597-023-02514-3.


The Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for the description of Avida, the most widely used computational approach for performing experimental evolution using digital organisms-self-replicating computer programs that evolve within a user-defined computational environment. The lack of a clearly defined vocabulary makes some biologists feel reluctant to embrace the field of digital evolution. This integrated framework empowers biologists by equipping them with the necessary tools to explore and analyze the field of digital evolution more effectively. By leveraging the vocabulary of Avida, researchers can gain deeper insights into the evolutionary processes and dynamics of digital organisms. In addition, OntoAvida allows researchers to make inference based on certain rules and constraints, facilitate the reproducibility of in silico evolution experiments and trace the provenance of the data stored in avidaDB-an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms. OntoAvida is part of the Open Biological and Biomedical Ontologies (OBO Foundry) and is available at http://www.obofoundry.org/ontology/ontoavida.html .