DatumKB

DatumKB compiles manually curated experimental results on the function and regulation of human proteins in cultured cells into structured "datums" to support evidence-based computational modeling and analysis.

Key Features:

• Manually Curated Data: Entries are derived from biological research literature and curated manually to ensure accuracy and reliability.
• Datum Format: Experimental results are stored as concise "datums," a standardized shorthand originally developed for the Pathway Logic model (STM8) for modeling intracellular signal transduction processes.
• Controlled Vocabulary: A controlled vocabulary is employed to ensure consistency and clarity in data representation.
• Cross-References: DatumKB integrates identifiers and links to HGNC, UniProt, PubChem, and Cellosaurus for comprehensive cross-referencing.
• Export Formats: Data are provided in the original datum format, simplified text, and JSON.
• Traceability: Each datum is linked to its literature source to support transparency and verifiability.

Scientific Applications:

• Evidence-based Modeling: Datums serve as evidence inputs for computational models such as the Pathway Logic model to analyze intracellular signaling and regulatory pathways.
• Data Interrogation and Analysis: The structured datums and cross-references enable extraction of specific experimental observations for hypothesis testing and experimental validation.

Methodology:

Experimental results are extracted from scientific literature, encoded into a standardized shorthand datum language (developed for Pathway Logic STM8), manually curated, stored as concise datums to enable efficient storage and retrieval, and each datum is traceable to its source.