The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

Mansheng Li,Fuchu He,Tao Chen,Chunyuan Yang,Yunping Zhu,Jie Ma,Qiang He

doi:10.1186/s12864-021-07827-4

Mansheng Li, Fuchu He + Show 5 more

Open Access

https://doi.org/10.1186/s12864-021-07827-4

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Abstract

BackgroundWith the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that contains temporal and spatial vocabularies is urgently needed to clarify PPI biological annotations. In this paper, we propose a precisely designed schema - PPIO (PPI Ontology) for representing the biological context of PPIs.ResultsInspired by the event model and the distinct characteristics of PPI events, PPIO consists of six core aspects of the information required for reporting a PPI event, including the interactor (who), the biological process (when), the subcellular location (where), the interaction type (how), the biological function (what) and the detection method (which). PPIO is implemented through the integration of appropriate terms from the corresponding vocabularies/ontologies, e.g., Gene Ontology, Protein Ontology, PSI-MI/MOD, etc. To assess PPIO, an approach based on PPIO in developed to extract PPI biological annotations from an open standard corpus “BioCreAtIvE-PPI”. The experiment results demonstrate PPIO’s high performance, a precision of 0.69, a recall of 0.72 and an F-score of 0.70.ConclusionsPPIO is a well-constructed essential ontology in the interpretation of PPI biological context. The results of the experiments conducted on the BioCreAtIvE corpus demonstrate that PPIO is able to facilitate PPI annotation extraction from biomedical literature effectively and enrich essential annotation for PPIs.

Highlights

With the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that contains temporal and spatial vocabularies is urgently needed to clarify PPI biological annotations
To better represent the temporal and spatial PPI information, we proposed an event-centered PPI ontology (PPIO) including six subontologies, i.e., interactors, biological processes, subcellular locations, interaction types, biological functions and detection methods
The “biological role” subclass describes the role played by the protein, e.g., “regulator” or “acceptor”, whereas the “protein state” subclass describes the state of the protein, e.g., modification state, phosphorylation or ubiquitination, when PPI occurs

Summary

Introduction

With the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that contains temporal and spatial vocabularies is urgently needed to clarify PPI biological annotations. Many ontologies in the biomedical field have emerged for knowledge representation, data exchange, database design, information retrieval, information extraction, etc. Their subjects range from gene annotation to intricate biological network modeling. GO includes abundant vocabularies that describe temporalspatial characteristics of gene and gene products It does not represent or capture the temporalspatial attributes specialized in PPI events. To capture the essence of PPI, this paper proposes an event-centered ontology, namely PPIO, to comprehensively represent the context of PPI, especially the temporal and spatial perspectives

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