SAPP

SAPP provides semantic annotation and provenance tracking of genomic data to enable FAIR-compliant interoperable genome analyses.

Key Features:

• Semantic Annotation: Automatic prediction, tracking, and storage of structural and functional genome annotations using Linked Data and Semantic Web technologies.
• Provenance Tracking: Management of provenance at both dataset- and element-wise levels, including recording of tools and versions used for annotations.
• RDF Data Model and Querying: Generation of a Resource Description Framework (RDF) genome data model that is queryable with SPARQL for complex, multi-level comparative analyses.
• Modular Design: Modular components support annotation, visualization, and export of genomic data into multiple formats.
• Interoperability and Reusability: Adherence to FAIR principles to ensure genome annotations are interoperable and reusable across platforms and studies.

Scientific Applications:

• Genome Annotation: Annotating de novo and existing genome assemblies with structural and functional annotations.
• Comparative Genomics: Large-scale, provenance-aware comparative analyses across datasets and annotation sources.
• Semantic Data Integration and Mining: Integration and advanced querying of genomic data using Semantic Web technologies and Linked Data formats.
• Provenance-driven Reproducibility: Tracking tool versions and provenance to support reproducibility and auditability of annotation results.

Methodology:

Implemented in Java for Unix-like systems; performs automatic prediction, tracking, and storage of structural and functional annotations in a Linked Data format, generates an RDF genome data model queryable with SPARQL, and manages provenance at dataset- and element-wise levels using Semantic Web technologies.