scholarly journals Information Content-Based Gene Ontology Semantic Similarity Approaches: Toward a Unified Framework Theory

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Gaston K. Mazandu ◽  
Nicola J. Mulder
Keyword(s):  
Gene Ontology ◽  
Information Content ◽  
Semantic Similarity ◽  
Experimental Evaluation ◽  
Similarity Measures ◽  
Mathematical Framework ◽  
Unified Framework ◽  
The Impact ◽  
Unified Description ◽  
Similarity Scores

Several approaches have been proposed for computing term information content (IC) and semantic similarity scores within the gene ontology (GO) directed acyclic graph (DAG). These approaches contributed to improving protein analyses at the functional level. Considering the recent proliferation of these approaches, a unified theory in a well-defined mathematical framework is necessary in order to provide a theoretical basis for validating these approaches. We review the existing IC-based ontological similarity approaches developed in the context of biomedical and bioinformatics fields to propose a general framework and unified description of all these measures. We have conducted an experimental evaluation to assess the impact of IC approaches, different normalization models, and correction factors on the performance of a functional similarity metric. Results reveal that considering only parents or only children of terms when assessing information content or semantic similarity scores negatively impacts the approach under consideration. This study produces a unified framework for current and future GO semantic similarity measures and provides theoretical basics for comparing different approaches. The experimental evaluation of different approaches based on different term information content models paves the way towards a solution to the issue of scoring a term’s specificity in the GO DAG.

scholarly journals GSAn: an alternative to enrichment analysis for annotating gene sets

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Aaron Ayllon-Benitez ◽  
Romain Bourqui ◽  
Patricia Thébault ◽  
Fleur Mougin
Keyword(s):  
Gene Ontology ◽  
Semantic Similarity ◽  
A Priori ◽  
Similarity Measures ◽  
Enrichment Analysis ◽  
Biological Information ◽  
Underlying Structure ◽  
Gene Set ◽  
Sequencing Technologies ◽  
Gene Coverage

Abstract The revolution in new sequencing technologies is greatly leading to new understandings of the relations between genotype and phenotype. To interpret and analyze data that are grouped according to a phenotype of interest, methods based on statistical enrichment became a standard in biology. However, these methods synthesize the biological information by a priori selecting the over-represented terms and may suffer from focusing on the most studied genes that represent a limited coverage of annotated genes within a gene set. Semantic similarity measures have shown great results within the pairwise gene comparison by making advantage of the underlying structure of the Gene Ontology. We developed GSAn, a novel gene set annotation method that uses semantic similarity measures to synthesize a priori Gene Ontology annotation terms. The originality of our approach is to identify the best compromise between the number of retained annotation terms that has to be drastically reduced and the number of related genes that has to be as large as possible. Moreover, GSAn offers interactive visualization facilities dedicated to the multi-scale analysis of gene set annotations. Compared to enrichment analysis tools, GSAn has shown excellent results in terms of maximizing the gene coverage while minimizing the number of terms.

scholarly journals A New Semantic Similarity Measure Based On Ontology for Movie Rate Prediction

2019 ◽  
Vol 8 (3) ◽  
pp. 6756-6762
Keyword(s):  
Semantic Similarity ◽  
Similarity Measure ◽  
Experimental Evaluation ◽  
Pearson Correlation ◽  
Similarity Measures ◽  
Similarity Score ◽  
Cosine Similarity ◽  
Semantic Similarity Measure ◽  
Rate Prediction ◽  
Target User

A recommendation algorithm comprises of two important steps: 1) Predicting rates, and 2) Recommendation. Rate prediction is a cumulative function of the similarity score between two movies and rate history of those movies by other users. There are various methods for rate prediction such as weighted sum method, regression, deviation based etc. All these methods rely on finding similar items to the items previously viewed/rated by target user, with assumption that user tends to have similar rating for similar items. Computing the similarities can be done using various similarity measures such as Euclidian Distance, Cosine Similarity, Adjusted Cosine Similarity, Pearson Correlation, Jaccard Similarity etc. All of these well-known approaches calculate similarity score between two movies using simple rating based data. Hence, such similarity measures could not accurately model rating behavior of user. In this paper, we will show that the accuracy in rate prediction can be enhanced by incorporating ontological domain knowledge in similarity computation. This paper introduces a new ontological semantic similarity measure between two movies. For experimental evaluation, the performance of proposed approach is compared with two existing approaches: 1) Adjusted Cosine Similarity (ACS), and 2) Weighted Slope One (WSO) algorithm, in terms of two performance measures: 1) Execution time and 2) Mean Absolute Error (MAE). The open-source Movielens (ml-1m) dataset is used for experimental evaluation. As our results show, the ontological semantic similarity measure enhances the performance of rate prediction as compared to the existing-well known approaches.

Impact of low-confidence interactions on computational identification of protein complexes

2020 ◽  
Vol 18 (04) ◽  
pp. 2050025
Author(s):  
Madhusudan Paul ◽  
Ashish Anand
Keyword(s):  
Semantic Similarity ◽  
Protein Complexes ◽  
Similarity Measures ◽  
Disease Diagnosis ◽  
False Positives ◽  
Detection Methods ◽  
Computational Techniques ◽  
Ppi Networks ◽  
Complex Detection ◽  
The Impact

Protein complexes are the cornerstones of most of the biological processes. Identifying protein complexes is crucial in understanding the principles of cellular organization with several important applications, including in disease diagnosis. Several computational techniques have been developed to identify protein complexes from protein–protein interaction (PPI) data (equivalently, from PPI networks). These PPI data have a significant amount of false positives, which is a bottleneck in identifying protein complexes correctly. Gene ontology (GO)-based semantic similarity measures can be used to assign a confidence score to PPIs. Consequently, low-confidence PPIs are highly likely to be false positives. In this paper, we systematically study the impact of low-confidence PPIs on the performance of complex detection methods using GO-based semantic similarity measures. We consider five state-of-the-art complex detection algorithms and nine GO-based similarity measures in the evaluation. We find that each complex detection algorithm significantly improves its performance after the filtration of low-similarity scored PPIs. It is also observed that the percentage improvement and the filtration percentage (of low-confidence PPIs) are highly correlated.

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