Uncertainty¶

A set of statistical measures of the value of an element.

An uncertainty collects the measures which belong together, for example the mean and the standard deviation of one experiment. Every measure appears at most once in it, so measures from another source belong into another uncertainty of the same element.

The measures do not affect a simulation. They say where a number comes from and how well it is known, which is what a reader of a published model wants to see and what a sampling of the parameters of a model needs.

The report shows every uncertainty as an element of its own, with the table of its measures and a link to the element it describes, and it shows the same table in the inspector of that element.

Attributes¶

Every element of a model also carries the common attributes of SBase.

uncertParameters

Every parameter names the statistic it describes, for example mean, standardDeviation, variance, sampleSize, a span such as confidenceInterval or range, or the distribution the value was drawn from. It gives the statistic either as a number in its value, or as a reference to an element of the model in its variable, and it may carry its own units. A parameter of the type distribution carries the math of the distribution or a definition url instead of a value; a parameter of the type externalParameter has to carry a definition url and may use everything else next to it, a value, a span, math or parameters of its own.

The report shows every parameter of an uncertainty as a row of the table in the inspector of that uncertainty, with its value or the interval of a span, its units, its definition and its math, and links every parameter to the element it is, where its notes say where the measurement comes from.

• 1520310 (error): Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfUncertParameters> container object may only contain <uncertParameter> objects.
• 1520403 (error): An <uncertainty> object may contain one and only one instance of the <listOfUncertParameters> element. No other elements from the SBML Level 3 Distributions namespaces are permitted on an <uncertainty> object.

Validation rules¶

• 1520401 (error): An <uncertainty> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespaces are permitted on an <uncertainty>.
• 1520402 (error): An <uncertainty> object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespaces are permitted on an <uncertainty>.
• 1520403 (error): An <uncertainty> object may contain one and only one instance of the <listOfUncertParameters> element. No other elements from the SBML Level 3 Distributions namespaces are permitted on an <uncertainty> object.

Related elements¶

• Parameter: a named value which the mathematics of the model can use
• Species: a pool of a chemical entity in a compartment
• Distributions (distrib): the package which records the uncertainty of a value

Specification¶

The Distributions Package for SBML Level 3, Version 1 Release 1, Section 3.10 (Smith et al. 2020, J Integr Bioinform 17(2-3):20200018).