mpath-ma

This folder contains the files needed to perform the following tasks:

Generating MAP, MAPT, PAM, PAMT ontologies:

for this task you can regenerate those ontologies using the generatePAM_MAP.groovy.

You can also specify the following optional arguments:

-m: to select MA ontology as a primary axis of classification for the ontology, if not selected it will be MPATH

-t: to select the transitivity option

to generate MAP :

generatePAM_MAP.groovy -m -o MAP.owl

to generate MAPT :

generatePAM_MAP.groovy -m -t -o MAPT.owl

to generate PAM :

generatePAM_MAP.groovy -o PAM.owl

to generate PAMT :

generatePAM_MAP.groovy -t -o PAMT.owl

OQuaRE measures:

To compute TMOnto, WMCOnto and DITOnto we used OQuaRE_measures.groovy

Compute semantic similarity:

To compute semantic similarity we used the following files:

MpathMAAnnotations.groovy to generate the annotations

piarwiseSimMpathMa.groovy to generate the mouse to mouse similarity matrix

Clustering, clustering purity, Area under purity curves:

we applied four methods for clustering in this analysis: complete linkage(CL), Unweighted Pair Group Method with Arithmetic Mean(UPGMA), neighbor joining(NJ) and K-medoids using the following files and folders:

clustering and statistical analysis/NJ_CL_UPGMA_clustering.m

clustering and statistical analysis/k_medoids_clustering.R

clustering and statistical analysis/similarities

clustering and statistical analysis/mice.csv

Kendall's tau:

we calculated Kendall's tau for the p-values generated by the enrichment analysis using the following files and folders:

clustering and statistical analysis/kendall.py

clustering and statistical analysis/EAcode

ROC and ROC AUC:

for plotting ROC curves and calculating ROC-AUC we used the following files and folders:

clustering and statistical analysis/ROC_curves_and_ROC_AUC.m

clustering and statistical analysis/similarities

clustering and statistical analysis/mice.csv

Wilcoxon rank sum test:

for calculating Wilcoxon rank sum test we used the following files and folders:

clustering and statistical analysis/wilcoxonSumRankTest.m

clustering and statistical analysis/similarities

clustering and statistical analysis/mice.csv