Towards a logic-based method to infer provenance-aware molecular networks

Zahira Aslaoui-Errafi; Sarah Cohen-Boulakia; Christine Froidevaux; Pauline Gloaguen; Anne Poupon; Adrien Rougny; Meriem Yahiaoui

Towards a logic-based method to infer provenance-aware molecular networks

Zahira Aslaoui-Errafi ^{1, 2} Sarah Cohen-Boulakia ^{1, 2} Christine Froidevaux ^{1, 2, *} Pauline Gloaguen ³ Anne Poupon ³ Adrien Rougny ^{1, 2} Meriem Yahiaoui ^{1, 2}

* Corresponding author

1 LRI - Laboratoire de Recherche en Informatique

2 AMIB - Algorithms and Models for Integrative Biology

LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France

3 PRC - Physiologie de la reproduction et des comportements [Nouzilly]

Abstract : Providing techniques to automatically infer molecular networks is particularly important to understand complex relationships between biological objects. We present a logic-based method to infer such networks and show how it allows inferring signalling networks from the design of a knowledge base. Provenance of inferred data has been carefully collected, allowing quality evaluation. More precisely, our method (i) takes into account various kinds of biological experiments and their origin; (ii) mimics the scientist's reasoning within a first-order logic setting; (iii) specifies precisely the kind of interaction between the molecules; (iv) provides the user with the provenance of each interaction; (v) automatically builds and draws the inferred network.

Document type :

Conference papers

Domain :

Computer Science [cs] / Bioinformatics [q-bio.QM]

Life Sciences [q-bio] / Quantitative Methods [q-bio.QM]

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Cited literature [23 references] Display Hide Download

https://hal.inria.fr/hal-00748041
Contributor : Sarah Cohen-Boulakia <>
Submitted on : Monday, November 12, 2012 - 11:38:52 AM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM
Document(s) archivé(s) le : Wednesday, February 13, 2013 - 2:45:09 AM

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