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SBGNlog: a logical framework based on SBGN to reason on molecular networks
Adrien Rougny

30 November 2017, 14:30
Salle/Bat : 435/PCRI-N
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Résumé :
The Systems Biology Graphical Notation (SBGN) is a standard that allows representing molecular networks in an unambiguous way.
SBGN maps can be stored and exchanged using the SBGN-ML format, and programmatically manipulated using the libSBGN library.
This latter was designed in order to ease the support (writing, reading, editing and validating) of SBGN maps in systems biology tools, and may not be perfectly suited to implement reasoning tasks on the biological knowledge the maps represent.
We will present a new framework, called SBGNlog, that facilitates the implementation of such tasks. SBGNlog is based on two first-order logic languages, namely SBGNlog PD and SBGNlog AF, that are the twins in logic of the PD and AF languages of SBGN. These two languages allow representing reaction networks (PD) and influence graphs (AF) into first-order logic, thus enabling the use of automated reasoning to solve a wide variety of reasoning tasks on those networks. Additionally, SBGNlog offers a user-friendly Python API interfacing the logic programming software clingo, that permits to easily implement those reasoning tasks, in a modular way.


Dans le cadre du groupe PSay CompBio, ouvert à tous.

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