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

Abstract

The commonly used Entity-Quality (EQ) syntax provides rich semantics and high granularity 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 aid production of fast annotations of characters and character matrices with biological ontologies. Its interactive interface allows quick and convenient tagging of character statements with necessary ontology terms. The annotations produced in ontoFAST can be exported in csv format for downstream analysis. Additinally, OntoFAST provides: (i) functions for constructing simple queries of characters against ontologies, and (ii) helper function for exporting and visualising complex ontological hierarchies and their relationships. OntoFAST enhances data interoperability between various applications and support further integration of ontological and phylogenetic methods. Ontology tools are underrepresented in R environment and we hope that ontoFAST will stimulate their further development.