enviPath - anonymous’ Package

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anonymous’ Package
Pathway

Create a new pathway by entering the root compound and a name. Then select if you want to use the prediction engine to generate a predicted pathway or create an empty pathway that you fill in by yourself. If you choose to predict a pathway, you can modify the settings for the prediction, or use the default settings and just click Submit.

Name Description

Predict pathway or build yourself?

Predict pathway

Incremental prediction

Build pathway

SMILES

Choose if you want to use an existing setting, or create a new one for this pathway prediction. Then click Submit to use the specified setting, or click next to set the parameters.

Use Default

Select Existing

Create New

To create a prediction setting, first choose a name and select the packages from which the rules for the prediction are used. When you are done, click Next.

Name

Select Packages

Next, select the Relative Reasoning object to use. If you do not see any relative reasoning object in the list, you have to train one first. Exit this menu and go to Relative Reasoning directly. You can also leave this empty and not use any relative reasoning models. When you chose the object, click Next.

Select Relative Reasoning Set the cutoff or select from the Precision-Recall curve

Evaluation Type

Finally, you can select the truncators. These can be based on the structure of the predicted pathway, like limiting the number of nodes to predict, e.g., limiting the depth of the pathway, or based on additional information of the transformation rules, e.g., the acidity in which the rule is working. By default, we included a limititaion on number of nodes and depth of the pathway, however, you can remove these limitations completely or replace them with other truncators. Note that if you are not logged in, the system sets the maximum number of nodes and maximum depth to a default value, independent of what you set here. When you are done, click Next, in the final step you will be able to review the setting.

Add truncator Type

Review the settings, if you are satisfied with your choice, click submit, if you want to modify anything, use the Back button to get back to the right window. If you just want to remove a certain entry, simply click the Remove button next to it.

Submit

Pathways

Actions

New Pathway

A pathway displays the (predicted) biodegradation of a compound as graph. Learn more >>

Unreviewed

Ad Caffeine Caffeine P > 0.1 Gabapentin Glutamate Salicylic acid Test test1