SPARQL

SPARQL queries and manipulates data in the Resource Description Framework (RDF) format to enable integration and comparative analysis of orthology and evolutionary relationships across RDF-based bioinformatics resources.

Key Features:

• RDF data querying and manipulation: Executes SPARQL queries to retrieve and manipulate triples stored in RDF data sources.
• Integration of multiple data sources: Combines orthology and evolutionary data from RDF-published resources such as The Orthologous MAtrix (OMA), the European Bioinformatics Institute (EBI) RDF platform, OrthoDB, and the Microbial Genome Database (MBGD).
• Federated queries: Supports federated SPARQL queries to query and join data across multiple RDF endpoints.
• Handling complex RDF models: Expresses queries across diverse RDF schemas and complex data models to capture hierarchical and relational orthology representations.

Scientific Applications:

• Orthology retrieval: Retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups from RDF-based databases.
• Comparative orthology analysis: Compare and reconcile orthology information across OMA, OrthoDB, MBGD, and EBI RDF resources using federated queries.

Methodology:

Formulate and execute SPARQL queries, including federated queries, against RDF endpoints to retrieve and combine orthology data such as pairwise orthologs, homologous groups, and hierarchical orthologous groups.