Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Metabolite Info Plugin

3,014 views

Published on

Published in: Technology
  • Be the first to comment

  • Be the first to like this

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?

×