Qualitative Models

The libSBML “qual” extension implements support for the SBML Level 3 Qualitative Models package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

Quantitative methods for modeling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modeling methods using information such as gene expression data coming from functional genomic experiments.

The qualitative models contemplated in this SBML Level 3 package for Qualitative Models are essentially based on the definition of regulatory or influence graphs. The components of these models differ from the species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. These systems can be viewed as reactive systems, whose dynamics are represented by means of state transition graphs (or other Kripke structures representing, in the form of a graph, which nodes are the reachable states and in which the edges are the state transitions). In this context, logical regulatory networks (Boolean or multi-valued) and standard Petri nets are the two formalisms mostly used in biology that give rise to such behaviors. Published models using these approaches cover, far from exhaustively, gene regulatory networks, signalling pathways and metabolic pathways.

Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support encoding qualitative models in SBML.

Authors

The primary authors of the SBML Level 3; Qualitative Models specification are Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel and Tomás̮Helikar.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Qualitative Models (“qual”) package. If you are developing software that uses “qual”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any). we apologise that our known issues pages are under reconstruction.

Specification for SBML Level 3 Qualitative Models, current at the time of this libSBML release (5.20.2). Note: an Internet connection is required to access these documents.

Specification (in PDF format)	Known issues
Qualitative Models package, Version 1 Release 1	Errata page

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Classes
class	DefaultTerm
class	FunctionTerm
class	Input
class	ListOfFunctionTerms
class	ListOfInputs
class	ListOfOutputs
class	ListOfQualitativeSpecies
class	ListOfTransitions
class	Output
class	QualExtension
class	QualitativeSpecies
class	QualModelPlugin
class	QualPkgNamespaces
class	QualSBMLDocumentPlugin
class	QualValidator
class	Transition

Detailed Description

The libSBML “qual” extension implements support for the SBML Level 3 Qualitative Models package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

Quantitative methods for modeling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modeling methods using information such as gene expression data coming from functional genomic experiments.

The qualitative models contemplated in this SBML Level 3 package for Qualitative Models are essentially based on the definition of regulatory or influence graphs. The components of these models differ from the species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. These systems can be viewed as reactive systems, whose dynamics are represented by means of state transition graphs (or other Kripke structures representing, in the form of a graph, which nodes are the reachable states and in which the edges are the state transitions). In this context, logical regulatory networks (Boolean or multi-valued) and standard Petri nets are the two formalisms mostly used in biology that give rise to such behaviors. Published models using these approaches cover, far from exhaustively, gene regulatory networks, signalling pathways and metabolic pathways.

Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support encoding qualitative models in SBML.

Authors

The primary authors of the SBML Level 3; Qualitative Models specification are Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel and Tomás̮Helikar.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Qualitative Models (“qual”) package. If you are developing software that uses “qual”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any). we apologise that our known issues pages are under reconstruction.

Specification for SBML Level 3 Qualitative Models, current at the time of this libSBML release (5.20.2). Note: an Internet connection is required to access these documents.

Specification (in PDF format)	Known issues
Qualitative Models package, Version 1 Release 1	Errata page