ontoavida.md

layout	id	title	browsers	contact	dependencies	description	domain	homepage	license	preferredPrefix	products	publications	repository	tags	tracker	usages	activity_status
ontology_detail	ontoavida	OntoAvida: ontology for Avida digital evolution platform	title label url Ontoavida HTML Browser Human-readable (HTML) https://owl.fortunalab.org/ontoavida/	email github label orcid fortuna@ebd.csic.es miguelfortuna Miguel A. Fortuna 0000-0002-8374-1941	id fbcv id gsso id ncit id ro id stato	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).	simulation	https://gitlab.com/fortunalab/ontoavida	label url CC BY 4.0 https://creativecommons.org/licenses/by/4.0/	ONTOAVIDA	id title description page ontoavida.owl OWL The main ontology in OWL https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.owl id title description page ontoavida.obo OBO Equivalent to ontoavida.owl, in obo format https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.obo	id title https://doi.org/10.1038/s41597-023-02514-3 Ontology for the Avida digital evolution platform	https://gitlab.com/fortunalab/ontoavida	digital evolution artificial life	https://gitlab.com/fortunalab/ontoavida/-/issues	description examples user An R package—avidaR—uses OntoAvida to perform complex queries on an RDF database—avidaDB—containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms description url avidaR: an R library to perform complex queries on an ontology-based database of digital organisms http://doi.org/10.7717/peerj-cs.1568 https://cran.r-project.org/package=avidaR	active

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.