Adding the values, Step 5

Adding the predicted values to a tabular view
of the dataset and downloading the table

When navigating to "our" dataset in Ambit2 (http://apps.ideaconsult.net:8080/ambit2/dataset/617343) we get the dataset content displayed. We would like, however, to include the predictions we have just calculated to the table view. This can be done by adding the feature URIs to the dataset URI:

For example:

Dataset URI: http://apps.ideaconsult.net:8080/ambit2/dataset/617343?page=0&pagesize=100 (we add the page and pagesize information here)
Feature URI: http://apps.ideaconsult.net:8080/ambit2/feature/22254

==> resulting URL: http://apps.ideaconsult.net:8080/ambit2/dataset/617343?page=0&pagesize=1...
Note that this way only the prediction feature is displayed for the dataset compound, but the original dataset content is not shown anymore.

To keep the original dataset content, start with the following:
Dataset URI including features: http://apps.ideaconsult.net:8080/ambit2/dataset/617343?page=0&pagesize=1...
Prediction feature URI: http://apps.ideaconsult.net:8080/ambit2/feature/22254

==> resulting URL: http://apps.ideaconsult.net:8080/ambit2/dataset/617343?page=0&pagesize=1...

To construct a table with all the predictions we have used, append all feature URIs to the above URL (add &feature_uris[]= before every feature URI). With all the models listed above, the resulting URL is the following:

http://apps.ideaconsult.net:8080/ambit2/dataset/617343?page=0&pagesize=1...

Display the dataset table with all the predictions in Ambit2 either by constructing the URL yourself, or by following the above URL.

If you have used additional models, add their feature URIs to the URL. In this step it is important to use the pagesize=100, since we will download the table. A pagesize of 10 will only download the 10 first compounds. Download the table in CSV format using the first "Excel" icon at the top of the table:

Open the downloaded table in your preferred spreadsheet viewer and investigate the data. Which compounds would you take forward to a next step in a drug discovery application? Which compounds would you eliminate from the list of drug candidates? For which compounds do you think more information is required?

PROCEED TO STEP 6:

Additional steps I) Applying an individual model to a dataset

STEPS:
Step 1: Creation of an OpenTox dataset from a local file
Step 2: Selection of models available in OpenTox through ToxPredict
Step 3: Application of the selected models to the uploaded dataset
Step 4: Obtaining simple statistics for the predictions obtained for the uploaded dataset
Step 5: Adding the predicted values to a tabular view of the dataset and downloading the table
Step 6: Additional steps I) Applying an individual model to a dataset
Step 7: Additional steps II) Searching a dataset according to prediction values
Step 8: Additional steps III) Obtaining additional predictions
Step 9: Additional steps IV) Downloading data from other dataset services in OpenTox
Step 10: Complement your findings with predicted associations with hepatobiliary adverse events

 

BACK TO Build a Weight of Evidence for Drug Candidate Molecules