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2016 | OriginalPaper | Buchkapitel

Metabolic Pathways as Temporal Logic Programs

verfasst von : Jean-Marc Alliot, Martín Diéguez, Luis Fariñas del Cerro

Erschienen in: Logics in Artificial Intelligence

Verlag: Springer International Publishing

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Abstract

Metabolic Networks, formed by series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell and by a set of interactions that guide and regulate the activity of these reactions. Cancers, for example, can sometimes appear in a cell as a result of some pathology in a metabolic pathway. Most of these pathways are formed by an intricate and complex network of chain reactions, and they can be represented in a human readable form using graphs which describe the cell signaling pathways.
In this paper we present a logic, called Molecular Equilibrium Logic, a nonmonotonic logic which allows representing metabolic pathways. We also show how this logic can be presented in terms of a syntactical subset of Temporal Equilibrium Logic, the temporal extension of Equilibrium Logic, called Splittable Temporal Logic Programs.

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Nächstes Kapitel On Decidability of a Logic of Gossips
Fußnoten
1
Regarding non-monotonic approaches to model biological systems, there are several contributions in the area of Answer Set Programming [9, 28], action languages [29] or Inductive Logic Programming [12]. In these contributions the temporal behaviour is considered in [29] but both representation and query languages are different.
 
2
The Nobel prize was awarded to Monod, Jacob and Lwoff in 1965 partly for the discovery of the lac operon by Monod and Jacob [18], which was the first genetic regulatory mechanism to be understood clearly, and is now a “standard” introductory example in molecular biology classes.
 
3
A less formal explanation can be found in https://​en.​wikipedia.​org/​wiki/​Lac_​operon.
 
4
It is important here to notice that lactose can be either considered as a weak endogenous variable, or as an exogenous variable if we consider that the environment is always providing “enough” lactose. It is a simple example which shows that variables in a graph can be interpreted differently according to what is going to be observed.
 
5
Notice that only the pathway formula associated with the production of Galactosidase has an associated context, defined in (1), while the rest of pathway formulas have an empty context.
 
6
Here and There [16] is an intermediate logic which severs as a monotonic basis for the Equilibrium Models [25], a logical characterisation of the Stable Model semantics [15].
 
7
Modal extensions of Equilibrium Logic and the logic of Here and There can be considered as promising lines of research which lead to several remarkable results, among others, [7, 13].
 
8
We refer the reader to [4] for details about the computation of such loop formulas.
 
9
We omitted the completion at time step 0 since the formula at the initial state depends on the extensional database, which is not considered here.
 
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Metadaten
Titel
Metabolic Pathways as Temporal Logic Programs
verfasst von
Jean-Marc Alliot
Martín Diéguez
Luis Fariñas del Cerro
Copyright-Jahr
2016
Buch
Logics in Artificial Intelligence

Print ISBN: 978-3-319-48757-1

Electronic ISBN: 978-3-319-48758-8

Copyright-Jahr: 2016

DOI
https://doi.org/10.1007/978-3-319-48758-8_1

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