Knowledge Base (KB) API

The VFB Knowledge Base (KB) is a specialized Neo4j database that complements the Production Database (PDB). While the PDB handles integrated ontology data, expression patterns, and image annotations, the KB serves specific VFB requirements and workflows.

Browser Access

Explore the KB using the Neo4j browser:

https://kb.virtualflybrain.org/browser/

Purpose and Scope

The KB serves as:

1. VFB-Specific Data Repository: Storage for VFB-specific annotations, metadata, and derived data
2. Workflow Support: Specialized storage supporting VFB curation and integration workflows

Note: Ontology data, expression patterns, image annotations, and connectivity data are stored in the Production Database (PDB).

Schema Requirements

The KB schema is designed with specific requirements:

• Updateability: Ontology terms and FlyBase features must be updateable via CI
• ID Stability: Derived class IDs (e.g., expression patterns) must be preserved during updates
• OWL Compatibility: Subset of content convertible to OWL using standard patterns
• Dataset Isolation: Ability to generate OWL files for individual datasets

Expression Patterns

Expression patterns in the KB follow the general semantic specification:

• Definition: Mereological sum of all cells in an anatomical structure expressing a gene/transgene
• Classification: Hierarchical organization via OWL reasoning
• Stability: IDs must remain stable across updates

Pattern Types

• Complete Expression Pattern: All cells in an organism expressing a gene
• Regional Expression Pattern: Subset of expression in specific anatomical regions

Integration with PDB

The KB and PDB work together in VFB’s data architecture:

• KB: Specialized storage for VFB-specific annotations, metadata, and derived data
• PDB: Integrated storage for ontology data, expression patterns, image annotations, connectivity data, and cross-referenced information
• Data Flow: VFB-specific data from KB supports curation and integration workflows alongside PDB data

Note: For queries involving ontology data, expression patterns, or image annotations, use the Production Database (PDB).

Maintenance and Updates

The KB is maintained through:

• Manual curation workflows
• Automated data loading pipelines
• Integration with external data sources
• Quality control and validation processes

For more details on the underlying schema, see the VFB Neo4j documentation.