PDBj

PDBj accepts and processes experimentally determined macromolecular structures, curates and distributes PDB data within the wwPDB, and converts PDB entries into PDB/RDF using OWL based on the PDB mmCIF Exchange Dictionary to enable Semantic Web integration.

Key Features:

• Archival curation: Accepts, processes, and archives experimentally determined macromolecular structures as a member of the wwPDB.
• PDB/RDF conversion: Transforms Protein Data Bank entries into PDB/RDF for semantic representation.
• OWL representation: Uses the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary to encode data semantics.
• Interoperability: Provides RDF/OWL-based data representations to enable integration with other biological information resources.
• Structure analysis services: Offers computational services and tools to analyze protein structures and relate macromolecular architecture to biological function.
• wwPDB collaboration: Participates in global data exchange and consistency within the worldwide Protein Data Bank (wwPDB) consortium.

Scientific Applications:

• Structural biology research: Supports bioinformatics and structural biology studies using curated macromolecular structures.
• Semantic data integration: Enables linking and querying of structural data across databases via RDF and OWL.
• Protein structure–function analysis: Facilitates analyses of relationships between macromolecular architecture and biological activity.
• Cross-dataset integrative analyses: Allows combining PDB structural data with diverse biological datasets for holistic investigations.

Methodology:

Acceptance and processing of experimentally determined macromolecular structures; conversion of PDB data into RDF (PDB/RDF); use of OWL based on the PDB mmCIF Exchange Dictionary.