GenEx_ontology

GenEx_ontology integrates semantic representations to enable federated semantic queries across heterogeneous biological databases for gene expression analysis.

Key Features:

• Ontology-Based Federated Approach: Uses an ontology-driven framework to integrate heterogeneous data stores and address syntactic and semantic heterogeneity.
• Semantic Model for Gene Expression (GenEx): Provides a semantic model tailored to represent gene expression consistently across platforms.
• Integration of Diverse Data Sources: Integrates Bgee (relational gene expression database), OMA (Orthologous Matrix in HDF5), and UniProtKB (RDF protein sequence and functional information).
• Relational-to-RDF Mappings and Virtual RDF Graphs: Transforms Bgee relational data into a virtual RDF graph instantiating the GenEx model and accessible via SPARQL.
• Materialized RDF for OMA: Expresses OMA data using the Orthology ontology as materialized RDF available through a SPARQL endpoint.
• Virtual Links for Federated Queries: Identifies and formally describes virtual links among integrated sources to enable joint federated queries.

Scientific Applications:

• Federated Querying: Enables complex SPARQL queries that span Bgee, OMA, and UniProtKB to combine gene expression, orthology, and protein functional data.
• Gene Expression and Functional Insight: Supports deriving insights into gene expression patterns and their functional implications across organisms.

Methodology:

Relational-to-RDF mappings create a virtual RDF graph for Bgee instantiating the GenEx model and exposed via a SPARQL endpoint; OMA data are expressed with the Orthology ontology and materialized as RDF served through a SPARQL endpoint; virtual links among sources are identified and formally described to enable joint queries.