AtlasRDF

AtlasRDF enables querying and integration of Gene Expression Atlas RDF data to analyze gene expression patterns across experimental factors such as diseases, cell types, compound treatments, pathways, and proteins.

Key Features:

• RDF Technology Integration: Utilizes the Resource Description Framework (RDF) to describe, publish, and link life science data for integration across datasets.
• Gene Expression Atlas Access: Provides programmatic access to the Gene Expression Atlas RDF data curated by the European Bioinformatics Institute (EBI) for queries by genes and experimental factors.
• Experimental Factor Ontology (EFO) Enrichment Analysis: Performs enrichment analysis of user-provided gene lists against the Experimental Factor Ontology background set to identify significant associations.
• Integrated Resource Exploration: Serves as an entry point to EBI integrated resources, enabling cross-dataset queries across diseases, cell types, compounds, pathways, and proteins.

Scientific Applications:

• Disease Research: Investigates gene expression patterns associated with specific diseases to support identification of biomarkers and disease-related expression signatures.
• Cell Type and Developmental Studies: Explores gene expression across cell types and developmental stages to characterize cellular functions and differentiation.
• Compound Treatment Analysis: Examines gene expression responses to compound treatments to inform studies of drug mechanisms and treatment-associated expression changes.

Methodology:

AtlasRDF leverages RDF to create a unified framework for data description and linkage and supports complex queries to extract patterns and relationships from Gene Expression Atlas RDF and linked EBI datasets.