oloPATH

Package for metabolomic pathways analysis.

Input data

oloPATH requires the following input data in CSV format:

1. data: is a matrix containing metabolite information, where rows represent metabolites and columns correspond to metabolite IDs (alignid), metabolite names (metabolite_name), metabolite InChiKeys (inchikey) and individual samples with their associated intensities.

alignid	metabolite_name	inchikey	C1	C2	C3	K1	K2	K3
1	Phenol sulfate	CTYRPMDGLDAWRQ-UHFFFAOYSA-N	37833	19019	2648536	127311	2368521	19525
2	Nicotinamide	DFPAKSUCGFBDDF-UHFFFAOYSA-N	122401	54811	418613	95612	101095	153269

2. study_design: is a table of two columns that associates study groups (group) with individual samples (sample).

group	sample
Control	C1
Control	C2
Control	C3
KO	K1
KO	K2
KO	K3

Species databases structure

Each database consists of three dictionaries: molecules, inchikey and pathways.

• molecules dictionary has ChEMI molecules identifiers as keys and dictionaries containing the molecule name, short InChiKey and associated Reactome pathways identfiers as values.

"molecules": {"10055": {"name": "Xamoterol",
                        "inchikey": "DXPOSRCHIDYWHW",
                        "pathways": ["R-HSA-162582",
                                     "R-HSA-372790",
                                     "R-HSA-373076",
                                     "R-HSA-375280",
                                     "R-HSA-390696",
                                     "R-HSA-500792"]
                       }
             }

• inchikey dictionary has short InChiKey as keys and lists containing the ChEMI identifiers associated as values.

"inchikey": {"DXPOSRCHIDYWHW": ["10055"]}

• pathways dictionary has Reactome pathways identifiers as keys and dictionaries containing the pathway name as values.

"pathways": {"R-HSA-162582": {"name": "Signal Transduction"},
             "R-HSA-372790": {"name": "Signaling by GPCR"},
             "R-HSA-373076": {"name": "Class A/1 (Rhodopsin-like receptors)"},
             "R-HSA-375280": {"name": "Amine ligand-binding receptors"},
             "R-HSA-390696": {"name": "Adrenoceptors"},
             "R-HSA-500792": {"name": "GPCR ligand binding"}
            }