CharProtDB

CharProtDB provides experimentally supported functional annotations of biochemically characterized proteins to enable accurate protein function assignment in genomics and proteomics analyses.

Key Features:

• Curated content: Manually curated entries of biochemically characterized proteins assembled through literature curation by JCVI (formerly TIGR) during prokaryotic genome sequencing projects.
• Direct functional assignments: Records emphasize direct (non-transitive) functional assignments rather than homology-based annotations.
• Integrated records: Selected records from publicly available protein collections are imported based on explicit biocuration criteria.
• Annotation types: Annotations include gene names, gene symbols, Gene Ontology (GO) terms, Enzyme Commission (EC) numbers, and TransportDB accessions.
• Provenance: Each annotation is cited to a journal reference or, for imported records lacking direct references, to the original database source.
• Support for automated workflows: Data are provided to support automated annotation pipelines and improve the reliability of automated protein annotation.

Scientific Applications:

• Automated annotation pipelines: Serve as a source of experimentally validated functional assignments for automated genome and proteome annotation workflows.
• Genomics and proteomics research: Provide experimentally supported protein function data for analyses of prokaryotic genomes and proteomic studies.
• Annotation provenance and traceability: Enable tracing of functional assertions to primary literature or original database sources for validation and curation tasks.

Methodology:

Manual literature curation by JCVI staff during prokaryotic genome sequencing projects; selective import of records from public protein collections based on biocuration criteria; annotations encoded with GO, EC and TransportDB accessions and cited to journal references or original database sources.