Metabolite Info Plugin For Pathvisio

Rianne Fijten

Idea

● Create a plugin for PathVisio that gives information for a selected metabolite– ID information, bruto formula, etc. (Standard

Pathvisio Metabolite Database and Chemical Identifier Resolver)

– NMR data● peak lists of predicted NMR chemical shifts

– HMDB– Calculated by CDK

● link-outs to spectra on HMDB

– MS data (only link-outs to spectra on HMDB)

Requirements

● Metabolite with a correct HMDB ID● Metabolite Database

When opening PathVisio

How the plugin works

Molecular propertiesfrom metabolitedatabase:● Name● ID● MF● SMILESFrom Chemical IdentifierResolver● Inchi● Inchi Key

Mass SpectroscopyImages from HMDB database● Low energy● Medium energy● High energy

How the plugin works

1H NMR peak list and spectrum image from HMDB database

13C NMR peak list and spectrum image from HMDB database● Carbon No.● CHn● Chemical shift● Conf. Limits● Average Exp.

13C NMR peak list generated by CDK● Carbon No.● Neighbors● Chemical shift

Error Messages

● When the ID is not an HMDB ID– “This plugin needs an HMDB ID to work”

● When the metabolite does not have a correct HMDB ID– “This HMDB ID was not recognized”

● When no metabolite database is selected– “Please select a metabolite database”

Error Messages

● When IDs could not be found– “Unknown”

● When NMR chemical shift could not be calculated– “No prediction available for HOSE code **”

● When an error occurs in the HMDB peak lists, they are not shown

Ideas For Future Adjustments

● Tab containing data for all metabolites in pathway when nothing is selected

● Creating separate tabs for NMR and MS data● Adding CDK-generated molecular images● Other CDK implementations

Questions?