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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 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
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
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?

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Metabolite Info Plugin

  • 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
  • 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