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Bioinformatics. 2018 Nov 30. doi: 10.1093/bioinformatics/bty988. [Epub ahead of print]

PPaxe: easy extraction of protein occurrence and interactions from the scientific literature.

Author information

Computational Genomics Lab; Genetics, Microbiology & Statistics Dept.; Universitat de Barcelona; Institut de Biomedicina (IBUB) Barcelona, Catalonia, Spain.



Protein-protein interactions (PPIs) are very important to build models for understanding many biological processes. Although several databases hold many of these interactions, exploring them, selecting those relevant for a given subject, and contextualizing them can be a difficult task for researchers. Extracting PPIs directly from the scientific literature can be very helpful for providing such context, as the sentences describing these interactions may give insights to researchers in helpful ways.


We have developed PPaxe, a python module and a web application that allows users to extract PPis and protein occurrence from a given set of PubMed and PubMedCentral articles; It presents the results of the analysis in different ways to help researchers export, filter and analyze the results easily.


PPaxe web demo is freely available at All the software can be downloaded from, including a command-line version and docker containers for an easy installation.

Supplementary Information:

Supplementary data are available at Bioinformatics online.

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