Dataset Information

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 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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07827-4.

SUBMITTER: Li M

PROVIDER: S-EPMC8596923 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundMany crucial cellular operations such as metabolism, signalling, and regulations are based on protein-protein interactions. However, the lack of robust protein-protein interaction information is a challenge. One reason for the lack of solid protein-protein interaction information is poor agreement between experimental findings and computational sets that, in turn, comes from huge false positive predictions in computational approaches. Reduction of false positive predictions and enhancing true positive fraction of computationally predicted protein-protein interaction datasets based on highly confident experimental results has not been adequately investigated.ResultsGene Ontology (GO) annotations were used to reduce false positive protein-protein interactions (PPI) pairs resulting from computational predictions. Using experimentally obtained PPI pairs as a training dataset, eight top-ranking keywords were extracted from GO molecular function annotations. The sensitivity of these keywords is 64.21% in the yeast experimental dataset and 80.83% in the worm experimental dataset. The specificities, a measure of recovery power, of these keywords applied to four predicted PPI datasets for each studied organisms, are 48.32% and 46.49% (by average of four datasets) in yeast and worm, respectively. Based on eight top-ranking keywords and co-localization of interacting proteins a set of two knowledge rules were deduced and applied to remove false positive protein pairs. The 'strength', a measure of improvement provided by the rules was defined based on the signal-to-noise ratio and implemented to measure the applicability of knowledge rules applying to the predicted PPI datasets. Depending on the employed PPI-predicting methods, the strength varies between two and ten-fold of randomly removing protein pairs from the datasets.ConclusionGene Ontology annotations along with the deduced knowledge rules could be implemented to partially remove false predicted PPI pairs. Removal of false positives from predicted datasets increases the true positive fractions of the datasets and improves the robustness of predicted pairs as compared to random protein pairing, and eventually results in better overlap with experimental results.