Datanator

Datanator provides an integrated database of genomic and biochemical measurements, including metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction rate constants, to enable retrieval of molecular and reaction data across organisms and environmental conditions for integrative biochemical research and mechanistic model construction.

Key Features:

• Integrated Database: Consolidates metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction rate constants from multiple sources into a single dataset.
• Data Clouds: Extracts "clouds" of related data for specific molecules or reactions and identifies chemically-similar molecules and phylogenetically-related organisms in comparable conditions.
• Data Manipulation Tools: Provides a REST API and computational tools for filtering, visualization, and exporting data.

Scientific Applications:

• Mechanistic model construction: Supplies molecular measurements and parameters for building and calibrating mechanistic models.
• Whole-cell modeling: Aggregates diverse molecular measurements to support construction and parameterization of whole-cell models.
• Comparative studies: Enables comparative analyses across organisms and environmental conditions using consolidated measurements and phylogenetic relationships.
• Meta-analysis and integrative analyses: Facilitates meta-analyses and integrative studies that span multiple biochemical subsystems.

Methodology:

Integrates molecular data from several databases and numerous publications into a consolidated resource.