Empusa

Empusa generates code to enforce consistency and provenance-aware representation of genome annotations in RDF using the Genome Biology Ontology Language (GBOL), OWL, and Shape Expressions (ShEx).

Key Features:

• Provenance-Aware Annotation: Incorporates data provenance into genome annotations via GBOL so each annotation includes contextual details and derivation history.
• Interoperability and Consistency: Links GBOL with existing ontologies to provide modular, extensible, and consistent representations of genomic entities, properties, and relationships.
• Formalized Information Models: Uses formalized information models within GBOL to standardize the representation and exchange of genomic data across datasets.
• Ontology and Graph Structure Integration: Employs OWL and ShEx to describe and validate graph structures of genome annotations, enforcing consistency within and between GBOL definitions.
• Serialization and Text Generation: Provides modules for serializing linked data to RDF and generating plain text files for downstream access and manipulation.

Scientific Applications:

• Large-scale comparative analyses: Enables consistent annotation across genomes to support large-scale comparative genomics studies.
• Automated annotation review: Facilitates review and validation of automatically generated genome annotations at scale by enforcing structural and provenance constraints.
• Provenance tracking and validation: Supports detailed tracking of annotation derivation to validate findings and facilitate collaborative genomics research.

Methodology:

Uses GBOL for provenance-aware modeling, OWL and ShEx to describe and validate ontology and graph structure, and modules to serialize linked data to RDF and generate plain text files.