The Variant Impact Reporting Ontology (VIRO) is an application ontology for describing pathogen mutations, their functional effects, and links to literature evidence. This will eventually be a slim of GenEpiO; I am currently working on getting the VIRO terms into GenEpiO itself.
The associated data specification can be found at https://github.com/cidgoh/pathogen-mutation-functionalannotation-package.
For more information about VIRO, please see my thesis: An ontology-based approach for modelling viral variant functional effects.
To use Ontofox from the command line, run this line from within src/ontology/imports:
curl -F file=@"general_ontofox.txt" -o general_import.owl https://ontofox.hegroup.org/service.php