1. Metabolite Info Plugin For Pathvisio
Rianne Fijten

2. 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)

3. Requirements
● Metabolite with a correct HMDB ID
● Metabolite Database

4. When opening PathVisio

5. How the plugin works
Molecular properties
from metabolite
database:
● Name
● ID
● MF
● SMILES
From Chemical Identifier
Resolver
● Inchi
● Inchi Key
Mass Spectroscopy
Images from
HMDB database
● Low energy
● Medium energy
● High energy

6. How the plugin works
1
H NMR peak list and
spectrum image from
HMDB database
13
C NMR peak list and
spectrum image from
HMDB database
● Carbon No.
● CHn
● Chemical shift
● Conf. Limits
● Average Exp.
13
C NMR peak list
generated by CDK
● Carbon No.
● Neighbors
● Chemical shift

7. 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”

8. 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

9. 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

10. Questions?