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A new method for measuring the semantic similarity on gene ontology

Ying Shen, Shaohong Zhang, Hau-San Wong
2010 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
The proposed algorithm searches for the shortest path that connects two terms and uses the sum of weights on the shortest path to compute the semantic similarity for GO terms.  ...  In this paper, a novel method, namely the Shortest Path (SP) algorithm, for measuring the semantic similarity on GO is proposed based on both the GO structure information and the term's property.  ...  To address these drawbacks, we propose a new hybrid method, namely the Shortest Path (SP) algorithm, to measure the semantic similarity over terms in GO.  ... 
doi:10.1109/bibm.2010.5706623 dblp:conf/bibm/ShenZW10 fatcat:zrbjipdq5bco3nnjaprwk4rpti

A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets

Aarón Ayllón-Benítez, Fleur Mougin, Julien Allali, Rodolphe Thiébaut, Patricia Thébault, Robert Hoehndorf
2018 PLoS ONE  
In this work, we propose a new method for analyzing the impact of different semantic similarity measures on gene set annotations.  ...  OPEN ACCESS Citation: Ayllón-Benítez A, Mougin F, Allali J, Thiébaut R, Thébault P (2018) A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets.  ...  Investigated semantic similarity measures. Pesquita et al. proposed a survey of semantic similarity measures to compare the terms in the context of GO [10] .  ... 
doi:10.1371/journal.pone.0208037 fatcat:k264k22i3ragxmklzz4ctjalee

A novel insight into Gene Ontology semantic similarity

Yungang Xu, Maozu Guo, Wenli Shi, Xiaoyan Liu, Chunyu Wang
2013 Genomics  
to measure the semantic similarity of GO terms and further compare the functional similarity of proteins.  ...  Using human ratings and a benchmark dataset, SSDD was found to improve upon existing methods for computing the semantic similarity of GO terms.  ...  Methods Inspired by developmental biology, we propose a new IC-independent hybrid method for computing the semantic similarity of GO terms from a novel perspective.  ... 
doi:10.1016/j.ygeno.2013.04.010 pmid:23628645 fatcat:dsvbppz27bb5pm4il2zo52ikce

Semantic Similarity over Gene Ontology for Multi-Label Protein Subcellular Localization

Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung
2013 Engineering  
A support vector machine (SVM) classifier with a new decision scheme is proposed to classify the multi-label GO semantic similarity vectors.  ...  The semantic similarity between GO terms is used to formulate semantic similarity vectors for classification.  ...  Semantic Similarity Measure To obtain the GO semantic similarity between two proteins, we should start by introducing the semantic similarity between two GO terms.  ... 
doi:10.4236/eng.2013.510b014 fatcat:5lc53bozwnee5hvwfszkjssl74

A New Path Length Measure Based on GO for Gene Similarity with Evaluation using SGD Pathways

Anurag Nagar, Hisham Al-Mubaid
2008 2008 21st IEEE International Symposium on Computer-Based Medical Systems  
We propose a new method for measuring the semantic similarity of genes based on path length between their annotation terms in the Gene Ontology.  ...  The non-linear measure ensures that the semantic similarity decreases with distance and proves to be quite competitive when compared to other measures.  ...  "A new method to measure the semantic similarity of GO terms." Bioinformatics, 2007. [16] Li Y., Bandar Z.A, and McLean D.  ... 
doi:10.1109/cbms.2008.27 dblp:conf/cbms/NagarA08 fatcat:5ksoi276pjdezjzfxz2bpooh4q

Effectively integrating information content and structural relationship to improve the GO-based similarity measure between proteins [article]

Bo Li, James Z. Wang, F. Alex Feltus, Jizhong Zhou, Feng Luo
2010 arXiv   pre-print
In this paper, we propose a new similarity measure, information coefficient similarity measure (SimIC), to effectively integrate both the information content (IC) of GO terms and the structural information  ...  Integrating IC and structural information of GO hierarchy can improve the effectiveness of the semantic similarity measure of GO terms.  ...  Results In this paper, we propose a new similarity measure, information coefficient similarity measure (Sim IC ), to effectively integrate both the information content (IC) of GO terms and the structural  ... 
arXiv:1001.0958v2 fatcat:jv2aqokcljdulfunqyylecti3a

A Topology-Based Metric for Measuring Term Similarity in the Gene Ontology

Gaston K. Mazandu, Nicola J. Mulder
2012 Advances in Bioinformatics  
We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on  ...  In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated  ...  Many thanks to the authors of the freely available libraries, in particular, the GO Consortium who made this work possible.  ... 
doi:10.1155/2012/975783 pmid:22666244 pmcid:PMC3361142 fatcat:rath4f6d75eynkhup7c3sua5si

A web tool for measuring gene semantic similarities by combining gene ontology and gene co-function networks

Jiajie Peng, Hongxiang Li, Yadong Wang, Jin Chen
2015 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '15  
We provide a working demonstration of a web tool that calculates functional similarities between GO terms by integrating gene co-function networks and information from GO.  ...  We demonstrate the function of the web tool by comparing remote GO terms.  ...  In order to accurately measure the functional similarities between genes, we recently developed a new method called NETSIM to measure GO based gene functional similarities by incorporating co-function  ... 
doi:10.1145/2808719.2816835 dblp:conf/bcb/PengLWC15 fatcat:svvwp6x5j5dxlhtiisra5i4iba

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

G. Yu, F. Li, Y. Qin, X. Bo, Y. Wu, S. Wang
2010 Bioinformatics  
GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.  ...  The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis  ...  In the Wang's method, the semantics of GO terms are encoded into a numeric format and the different semantic contributions of the distinct relations are considered.  ... 
doi:10.1093/bioinformatics/btq064 pmid:20179076 fatcat:w7tkaxqecbealfy2iahujexedu

Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method

Xiaomei Wu, Erli Pang, Kui Lin, Zhen-Ming Pei, Peter Csermely
2013 PLoS ONE  
Explicit comparisons based on the semantic similarity of Gene Ontology terms provide a quantitative way to measure the functional similarity between gene products and are widely applied in large-scale  ...  However, edge-based semantic similarity metrics are sensitive to the intrinsic structure of GO and simply consider terms at the same level in the ontology to be equally specific nodes, revealing the weaknesses  ...  Wrote the paper: XW.  ... 
doi:10.1371/journal.pone.0066745 pmid:23741529 pmcid:PMC3669204 fatcat:n6g5ms6irrdflksxivpukricyy

Inferring unknown biological function by integration of GO annotations and gene expression data [article]

Guillermo Leale, Ariel Bayá, Diego Milone, Pablo Granitto and Georgina Stegmayer
2016 arXiv   pre-print
We provide a method to explore the potential function of new genes according to those currently annotated.  ...  Thus, it is possible to take advantage of clustering techniques to obtain groups of unknown genes that are co-clustered with genes that have well-known semantic information (GO annotations).  ...  A new measure for gene clustering: the gamma distance Based on the expression and semantic distances described above, a new distance that takes into account both will be used here [31] .  ... 
arXiv:1608.03672v1 fatcat:25bvfjozo5g5xe2t6ksxfmnzxi

A Weighted Multipath Measurement Based on Gene Ontology for Estimating Gene Products Similarity

Lizhen Liu, Xuemin Dai, Hanshi Wang, Wei Song, Jingli Lu
2014 Journal of Computational Biology  
We propose a new method called weighted multipath measurement (WMM) for estimating the semantic similarity of gene products based on the structure of the GO.  ...  Many different methods have been proposed for calculating the semantic similarity of term pairs based on gene ontology (GO).  ...  ACKNOWLEDGMENTS This work was supported in part by the National Science Foundation of China under  ... 
doi:10.1089/cmb.2014.0143 pmid:25229994 pmcid:PMC4253309 fatcat:ul6fx5taazbuxizhzxsk6n5ol4

Exploiting Biomedical Web Resources: A Case Study

Nicoletta Dessì, Barbara Pes
2016 Procedia Computer Science  
Due to the GO structure and content, results reveal limitations that not affect the evaluation of the semantic similarity when genes exhibit simple correlations but influence the estimation of the relatedness  ...  Within this context, Gene Ontology (GO) is a popular and effective mean for extracting knowledge from a list of genes and evaluating their semantic similarity.  ...  Tailored to the characteristics of GO, new semantic similarity measures are constantly appearing in the literature 15, 16 .  ... 
doi:10.1016/j.procs.2016.09.043 fatcat:ffbo43bftbcn7hzweijbtpy75q

A density-based approach for detecting complexes in weighted PPI networks by semantic similarity

HongFang Zhou, Jie Liu, JunHuai Li, WenCong Duan, Byung-Jun Yoon
2017 PLoS ONE  
Firstly, a method based on gene ontology is used to measure semantic similarities between interacted proteins, and the similarity values are used as their weights.  ...  Then, a density-based graph partitioning algorithm is developed to find clusters in the weighted PPI networks, and the identified ones are considered to be dense and similar.  ...  Acknowledgments We would like to acknowledgment three reviewers for helpful suggestions. Author Contributions Conceptualization: HongFang Zhou.  ... 
doi:10.1371/journal.pone.0180570 pmid:28704455 pmcid:PMC5507511 fatcat:qnrqm2o6gbazhod33vsf753elu

TopoICSim: a new semantic similarity measure based on gene ontology

Rezvan Ehsani, Finn Drabløs
2016 BMC Bioinformatics  
Generally speaking, semantic similarity measures involve the GO tree topology, information content of GO terms, or a combination of both.  ...  Results: Here we present a new semantic similarity measure called TopoICSim (Topological Information Content Similarity) which uses information on the specific paths between GO terms based on the topology  ...  The GO consortium updates on a regular basis a GO Annotation (GOA) [3] database with new GO terms that are linked to genes and gene products by relevant studies.  ... 
doi:10.1186/s12859-016-1160-0 pmid:27473391 pmcid:PMC4966780 fatcat:ff4opvuk4ne4vbpfbrsn5jxd24
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