ontoFAST

ontoFAST facilitates interactive and semi-automatic annotation of biological characters with ontologies in R to support phenotype and character-matrix analyses.

Key Features:

• R implementation: Implemented as an R package for integration with R-based analytical workflows.
• Interactive and semi-automatic annotation: Supports interactive and semi-automatic tagging of character statements with ontology terms.
• Fast annotation production: Optimized for rapid annotation production when Entity-Quality (EQ) syntax granularity is unnecessary.
• Export functionality: Exports annotations in CSV format for downstream analysis and interoperability.
• Query construction: Provides functions to construct simple queries of characters against ontologies.
• Visualization tools: Includes functions to export and visualize ontological hierarchies and relationships.

Scientific Applications:

• Phenotype and character-matrix annotation: Annotating phenotypic characters and character matrices with ontology terms.
• Evolutionary biology and systematics: Supporting trait annotation and comparison in evolutionary biology and systematics studies.
• Phylogenetics integration: Enabling integration of ontological annotations with phylogenetic methods.

Methodology:

Implemented in R; provides semi-automatic annotation workflows, functions to export annotations to CSV, construct character-to-ontology queries, and export/visualize ontological hierarchies; optimized for fast annotation when Entity-Quality (EQ) syntax is not required.