Metabolite Info Plugin For Pathvisio             Rianne Fijten
Idea●   Create a plugin for PathVisio that gives    information for a selected metabolite    –   ID information, bruto for...
Requirements●   Metabolite with a correct HMDB ID●   Metabolite Database
When opening PathVisio
How the plugin works                  Molecular properties                  from metabolite                  database:    ...
How the plugin works                  1                   H NMR peak list and                  spectrum image from        ...
Error Messages●   When the ID is not an HMDB ID    –   “This plugin needs an HMDB ID to work”●   When the metabolite does ...
Error Messages●   When IDs could not be found    –   “Unknown”●   When NMR chemical shift could not be    calculated    – ...
Ideas For Future Adjustments●   Tab containing data for all metabolites in    pathway when nothing is selected●   Creating...
Questions?
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Metabolite Info Plugin

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Metabolite Info Plugin

  1. 1. Metabolite Info Plugin For Pathvisio Rianne Fijten
  2. 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. 3. Requirements● Metabolite with a correct HMDB ID● Metabolite Database
  4. 4. When opening PathVisio
  5. 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. 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. 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. 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. 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. 10. Questions?

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