ontoFAST: An R package for interactive and semi-automatic annotation of characters with biological ontologies

Ontologies are becoming a fundamental technology for analysing phenotypic data. The commonly used Entity–Quality (EQ) provides rich semantics for annotating phenotypes and characters using ontologies. However, EQ syntax might be time inefficient if this granularity is unnecessary for downstream analysis. We present an R package ontoFAST that aids fast annotations of characters with biological ontologies. ontoFAST takes a biomedical ontology in OBO format and a list of characters as input, and produces a list of mappings from characters to ontology terms as output. The annotations produced by ontoFAST can be exported in CSV format for downstream analysis. Additionally, ontoFAST provides (a) functions for constructing simple queries of characters against ontologies and (b) helper function for exporting and visualizing complex ontological hierarchies and their relationships. ontoFAST enhances integration of ontological and phylogenetic methods and supports data interoperability between R applications. Ontology tools are underrepresented in R ecosystem and we hope that ontoFAST will stimulate their further development.