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Table 1 Selected information types supported in SigPath.

From: Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

Classes

Description

SmallMolecule

A small molecule, such as ATP

Complex

A binding complex between two or more molecules

Protein

A protein molecule

Chemical

A small molecule, protein or complex

Reaction

Reaction between molecules: has substrates and products

EnzymaticReaction

Associates a reaction to the enzyme that catalyze it

Unit

Represents a unit, such as mol/l or /sec

Parameter

Associates a value to its unit

ConcentrationMeasurement

Associates a concentration to a molecule and the conditions of the measurement

Pathway

A set of reactions and enzymatic reactions

Model

A quantitative biochemical model, a set of reactions (or enzymatic reactions), initial concentrations for molecules in the model, rates of the reaction, kinetic parameters of the enzymatic reactions.