| ontologySimilarity-package {ontologySimilarity} | R Documentation |
Functions for Calculating Ontological Similarities
Description
Functions for calculating semantic similarities between ontological terms or sets of ontological terms based on term information content and assessing statistical significance of similarity in the context of a collection of sets of ontological terms.
Details
Semantic similarity and similarity significance functions based on Resnik and Lin's measures of similarity. Computationally intensive functions are written in C++ for performance.
Author(s)
Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
References
Greene D, Richardson S, Turro E (2017). 'ontologyX: a suite of R packages for working with ontological data. _Bioinformatics_, 33(7), 1104–1106.
Westbury SK, Turro E, Greene D, Lentaigne C, Kelly AM, Bariana TK, Simeoni I, Pillois X, Attwood A, Austin S, Jansen SB, Bakchoul T, Crisp-Hihn A, Erber WN, Favier R, Foad N, Gattens M, Jolley JD, Liesner R, Meacham S, Millar CM, Nurden AT, Peerlinck K, Perry DJ, Poudel P, Schulman S, Schulze H, Stephens JC, Furie B, Robinson PN, Geet Cv, Rendon A, Gomez K, Laffan MA, Lambert MP, Nurden P, Ouwehand WH, Richardson S, Mumford AD and Freson K (2015). ‘Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders.’ _Genome Med_, *7*(1), pp. 36.
Kohler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jahn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout A, de Leeuw N, de Vries B, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE and Robinson PN (2014). ‘The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.’ _Nucleic Acids Res._, *42*(Database issue), pp. D966-974.
Resnik, P. (1995). ‘Using information content to evaluate semantic similarity in a taxonomy’. Proceedings of the 14th IJCAI 1, 448-453.
Lin D (1998). ‘An Information-Theoretic Definition of Similarity.’ In Shavlik JW (ed.), _Proceedings of the Fifteenth International Conference on Machine Learning (ICML 1998), Madison, Wisconsin, USA, July 24-27, 1998_, pp. 296-304.