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

Abstract Background 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. In this paper, we propose a precisely des...

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Autores principales:	Mansheng Li, Qiang He, Chunyuan Yang, Jie Ma, Fuchu He, Tao Chen, Yunping Zhu
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Protein-protein Interaction PPI Ontology PPI Annotation PPI Annotation Extraction Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/a84b411caaf246c595069b6c4e5e75e8
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spelling	oai:doaj.org-article:a84b411caaf246c595069b6c4e5e75e82021-11-21T12:26:23ZThe protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction10.1186/s12864-021-07827-41471-2164https://doaj.org/article/a84b411caaf246c595069b6c4e5e75e82021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-07827-4https://doaj.org/toc/1471-2164Abstract Background 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. In this paper, we propose a precisely designed schema - PPIO (PPI Ontology) for representing the biological context of PPIs. Results Inspired 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. Conclusions PPIO 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.Mansheng LiQiang HeChunyuan YangJie MaFuchu HeTao ChenYunping ZhuBMCarticleProtein-protein InteractionPPI OntologyPPI AnnotationPPI Annotation ExtractionBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss S5, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Protein-protein Interaction PPI Ontology PPI Annotation PPI Annotation Extraction Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Protein-protein Interaction PPI Ontology PPI Annotation PPI Annotation Extraction Biotechnology TP248.13-248.65 Genetics QH426-470 Mansheng Li Qiang He Chunyuan Yang Jie Ma Fuchu He Tao Chen Yunping Zhu The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
description	Abstract Background 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. In this paper, we propose a precisely designed schema - PPIO (PPI Ontology) for representing the biological context of PPIs. Results Inspired 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. Conclusions PPIO 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.
format	article
author	Mansheng Li Qiang He Chunyuan Yang Jie Ma Fuchu He Tao Chen Yunping Zhu
author_facet	Mansheng Li Qiang He Chunyuan Yang Jie Ma Fuchu He Tao Chen Yunping Zhu
author_sort	Mansheng Li
title	The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
title_short	The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
title_full	The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
title_fullStr	The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
title_full_unstemmed	The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
title_sort	protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction
publisher	BMC
publishDate	2021
url	https://doaj.org/article/a84b411caaf246c595069b6c4e5e75e8
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The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

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