The Name-IdMatchWizard (NIMWiz) plugin for PathVisio matches the metabolites/genes in a metabolite/gene dataset to known identifiers and can help you in that way with the creation of a suitable datafile for expression visualization or pathway creation (MAPPBuilder Plugin).
How to use NIMWiz as a PathVisio plugin:
Install NIMWiz by going to Plugins -> PluginManager. Select the NIMWiz plugin and click on install.
Note: If you are running NIMWiz as a Pathvisio Plugin and you’ve already loaded databases then these will be used for the plugin as well.
- Start Pathvisio, click Plugins -> NIMWiz.
- Choose whether you want to work with Metabolite data or Gene data.
- Select your tabdelimeted datafile (column header “Metabolite Name” / “Gene Name” prefered, otherwise you’ll have to select the right column later on).
- If there’s no (correct) identifier mapping database is loaded, a second dialog will pop up. Select the needed database file here.
Optional: You can also use the BridgeDbConfigPlugin to use multiple BridgeDb identifier mapping databases together. Use Data -> “Identifier mapping setup…”. Make sure only databases that you need for your dataset are loaded in PathVisio!
You will now see the main window:
Navigation: When the data table (upper table) is filled you can navigate trough it by simply clicking on the rows and using the scrollbars or by clicking the previous/next suggestion button that will show you the previous/next entry with available suggestions (Orange).
Confirm suggestion/add own input: You confirm a suggestion by double clicking it or selecting it and clicking the change button. If you do this at the last row of the table an input dialog will appear. Preferred Data source: All identifiers will be mapped to the data source you prefer if possible.
Skip: The selected row will be skipped.
Reset: The selected row will be resetted to his original values.
Undo: Last change will be undone.
Finish: Quits the plugin (saving is optional).