PPIntegrator: semantic integrative system for protein–protein interaction and application for host–pathogen datasets


Semantic web standards have shown importance in the last 20 years in promoting data formalization and interlinking between the existing knowledge graphs. In this context, several ontologies and data integration initiatives have emerged in recent years for the biological area, such as the broadly used Gene Ontology that contains metadata to annotate gene function and subcellular location. Another important subject in the biological area is protein–protein interactions (PPIs) which have applications like protein function inference. Current PPI databases have heterogeneous exportation methods that challenge their integration and analysis. Presently, several initiatives of ontologies covering some concepts of the PPI domain are available to promote interoperability across datasets. However, the efforts to stimulate guidelines for automatic semantic data integration and analysis for PPIs in these datasets are limited. Here, we present PPIntegrator, a system that semantically describes data related to protein interactions. We also introduce an enrichment pipeline to generate, predict and validate new potential host–pathogen datasets by transitivity analysis. PPIntegrator contains a data preparation module to organize data from three reference databases and a triplification and data fusion module to describe the provenance information and results. This work provides an overview of the PPIntegrator system applied to integrate and compare host–pathogen PPI datasets from four bacterial species using our proposed transitivity analysis pipeline. We also demonstrated some critical queries to analyze this kind of data and highlight the importance and usage of the semantic data generated by our system.

SEEK ID: https://workflowhub.eu/publications/26

DOI: 10.1093/bioadv/vbad067

Teams: yPublish - Bioinfo tools

Publication type: Journal

Journal: Bioinformatics Advances

Editors: Thomas Lengauer

Citation: Bioinformatics Advances 3(1),vbad067

Date Published: 2023

Registered Mode: by DOI

Authors: Yasmmin Côrtes Martins, Artur Ziviani, Maiana de Oliveira Cerqueira e Costa, Maria Cláudia Reis Cavalcanti, Marisa Fabiana Nicolás, Ana Tereza Ribeiro de Vasconcelos

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Martins, Y. C., Ziviani, A., Cerqueira e Costa, M. de O., Cavalcanti, M. C. R., Nicolás, M. F., & de Vasconcelos, A. T. R. (2023). PPIntegrator: semantic integrative system for protein–protein interaction and application for host–pathogen datasets. In T. Lengauer (Ed.), Bioinformatics Advances (Vol. 3, Issue 1). Oxford University Press (OUP). https://doi.org/10.1093/bioadv/vbad067

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Created: 23rd Oct 2023 at 15:18

Last updated: 23rd Oct 2023 at 15:21

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