Similarity of proteins based on semantic similarity. More...

Classes
class	CFunctionalSimilarityBase
	Functional similarity computation base class. More...

class	CFunctionalSimilarity
	Functional similarity computation using a database connection. More...

Variables
string	SIM_RESNIK = "resnik";
	Resnik's pairwise semantic similarity measure. More...

string	SIM_LIN = "lin";
	Lin's pairwise semantic similarity measure. More...

string	SIM_IC = "ic";
	Information coefficient pairwise semantic similarity measure. More...

string	SIM_GIC = "gic";
	Graph information content pairwise semantic similarity measure. More...

string	SIM_REL = "rel";
	Schlicker's pairwise semantic similarity measure. More...

string	SIM_JC = "jc";
	Jiang & Conarth's pairwise semantic similarity measure. More...

string	IC = "ICo";
	Information Content. More...

list	SS_MEASURES = [SIM_RESNIK, SIM_LIN, SIM_IC, SIM_GIC, SIM_REL, SIM_JC];
	List of all possible semantic similarity measures. More...

string	FUNSIM_AVG = "avg";
	Average of similarity matrix. More...

string	FUNSIM_MAX = "max";
	Max value of similarity matrix. More...

string	FUNSIM_RCAVGMAX = "rcavgmax";
	Maximum row/column averaged maxima of similarity matrix. More...

string	FUNSIM_BMA = "bma";
	Best match average of similarity matrix. More...

string	FUNSIM_BMA2 = "bma2";
	Best match average averaged of similarity matrix. More...

Detailed Description

Similarity of proteins based on semantic similarity.

Provides methods to compute functional similarity between UniProt identifiers using semantic similarity measures associated with proteins. The semantic similarity measures depend on an ontology.

Author: Chris X. Weichenberger

Date: 2014-05-22

Copyright: See LICENSE file.

Variable Documentation

◆ FUNSIM_AVG

string cls.FunctionalSimilarity.FUNSIM_AVG = "avg";

Average of similarity matrix.

◆ FUNSIM_BMA

string cls.FunctionalSimilarity.FUNSIM_BMA = "bma";

Best match average of similarity matrix.

◆ FUNSIM_BMA2

string cls.FunctionalSimilarity.FUNSIM_BMA2 = "bma2";

Best match average averaged of similarity matrix.

◆ FUNSIM_MAX

string cls.FunctionalSimilarity.FUNSIM_MAX = "max";

Max value of similarity matrix.

◆ FUNSIM_RCAVGMAX

string cls.FunctionalSimilarity.FUNSIM_RCAVGMAX = "rcavgmax";

Maximum row/column averaged maxima of similarity matrix.

◆ IC

string cls.FunctionalSimilarity.IC = "ICo";

Information Content.

◆ SIM_GIC

string cls.FunctionalSimilarity.SIM_GIC = "gic";

Graph information content pairwise semantic similarity measure.

◆ SIM_IC

string cls.FunctionalSimilarity.SIM_IC = "ic";

Information coefficient pairwise semantic similarity measure.

◆ SIM_JC

string cls.FunctionalSimilarity.SIM_JC = "jc";

Jiang & Conarth's pairwise semantic similarity measure.

◆ SIM_LIN

string cls.FunctionalSimilarity.SIM_LIN = "lin";

Lin's pairwise semantic similarity measure.

◆ SIM_REL

string cls.FunctionalSimilarity.SIM_REL = "rel";

Schlicker's pairwise semantic similarity measure.

◆ SIM_RESNIK

string cls.FunctionalSimilarity.SIM_RESNIK = "resnik";

Resnik's pairwise semantic similarity measure.

◆ SS_MEASURES

list cls.FunctionalSimilarity.SS_MEASURES = [SIM_RESNIK, SIM_LIN, SIM_IC, SIM_GIC, SIM_REL, SIM_JC];

List of all possible semantic similarity measures.

Classes

Variables