PaNTex: A novel methodology to assemble Pathway Networks using Text Mining

DUSSAUT, JULIETA S.; CRAVERO, FIORELLA; PONZONI, IGNACIO; MAGUITMAN, ANA G.; CECCHINI, ROCÍO L.

San Carlos de Bariloche

Conferencia; V Argentinean Conference on Computational Biology and Bioinformatics; 2014

Asociación Argentina de Bioinformática y Biología Computacional

In this work we present a literature mining approach for assisting in the construction of a pathway network. It is important to mention that our proposal is in an initial stage of development. For this reason, only the general architecture of the computational strategy and preliminary experiments are reported here. As a starting point of this approach, we use KEGG pathway database in order to gather a list of pathways for each organism, at this starting stage we consider only human and yeast as valid organisms for the method. Using this list we search PubMed publications via its Entrez Programming Utilities and look for co-occurrence of pathways in the same publication. The resulting data is stored in an intersection matrix. We also keep track of the number of publications that contain a pathway name to use for normalization purposes. In order to validate the proposed method we contrast the resulting normalized matrix with data reported by Alexeyenko & Sonnhammer.