Hello All, I am currently using the latest version of EnrichmentBrowser which is a great all-in-one package for RNAseq/Microarray experiments with simple contrast designs. However, the native functionality for pathways is limited to KEGG and the KGML format. I am by no means an expert coder (happy to learn) but would like to know if there is a
1) Format that already exists in Reactome that can be quickly parsed into KGML.
2) Coaxing Biopax organism .owl files into a similar .xml format as KEGG.
3) Repurposing existing 'converters'. Another user has asked this question before me previously but has not left a trail that I could follow (https://www.biostars.org/p/244434/). KEGG Translator (http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/) seems robust but I am not at a level where I can reverse engineer this program to do what I need. KCPAVs is reported to be able to handle this conversion but had 'connection failed' issues using their converter https://sites.google.com/a/cidms.org/kcpavs/home)