Abstract
Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The Systems Biology Markup Language (SBML) Level 3 Core specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Distributions package for SBML Level 3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.
Highlights
Introduction and motivation1.1 What is the Distributions package?The Distributions package provides an extension to Systems Biology Markup Language (SBML) Level 3 that extends MathML to 3 allow draws from distributions, and provides the ability to annotate model elements with information about 4 the distribution their values were drawn from.The Distributions package adds support to SBML for sampling from a probability distribution
In 2005, Colin Gillespie and others put forward a proposal 1 to introduce support for probability distributions in the SBML core specification
They proposed that distributions be referred to in SBML using the csymbol element in the MathML subset used by the SBML Core specification
Summary
The following table summarizes the history of this document. Added introductory text and background info. Incorporated comments from Nicolas, Maciej and Sarah. Incorporated revisions discussed and agreed at HARMONY 2012. Incorporated review comments from Maciej and Sarah. Incorporated changes suggested at combine and subsequently through list discussions. Incorporated corrections and comments from Maciej and Sarah. Modified based on Stuart’s proposals and PWG discussion. Lucian Smith and Modified based on HARMONY 2013 discussion. Lucian Smith and Modified based PWG discussion, with respect to UncertML. Lucian Smith and Modified to match UncertML 3.0 for real this time. Extensive update to reflect demise of UncertML 3.0, and appearance of ProbOnto. Revisions based on suggestions from sbml-distrib, including extensive edits from Matthias. February 2019 Lucian Smith and Removal of Distribution and all subclasses; replaced with a Math element.
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