avidaR: an R library to perform complex queries on an ontology-based database of digital organisms

Abstract

Digital evolution is a branch of artificial life in which self-replicating computer programs—digital organisms—mutate and evolve within a user-defined computational environment. In spite of its value in biology, we still lack an up-to-date and comprehensive database on digital organisms resulting from evolution experiments. Therefore, we have developed an ontology-based semantic database—avidaDB—and an R package—avidaR—that provides users of the R programming language with an easy-to-use tool for performing complex queries without specific knowledge of SPARQL or RDF. avidaR can be used to do research on robustness, evolvability, complexity, phenotypic plasticity, gene regulatory networks, and genomic architecture by retrieving the genomes, phenotypes, and transcriptomes of more than a million digital organisms available on avidaDB. avidaR is already accepted on CRAN (i.e., a comprehensive collection of R packages contributed by the R community) and will make biologists better equipped to embrace the field of digital evolution.

Keywords

• Artificial life
• Digital evolution
• Digital genetics
• Semantic database
• Ontology-based database
• Digital organism