RxMix Tutorial

Batch Example

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A Batch Example

In this example, the batch processing function of RxMix will be illustrated. In addition, the workflow configuration will be saved and loaded.

The application developed in this example will process a file of National Drug Codes (NDCs) and determine what conditions are treated by the drugs using the NDF-RT "may_treat" role. Specifically, the following functions are needed to accomplish this task:

findRxcuiById (RxNorm) to read the NDC and convert to an RxNorm concept identifier (RxCUI) of the drug.
getRelatedByType (RxNorm) to get the ingredient(s) of the drug.
findConceptsByName (NDF-RT) to get the NDF-RT concept for the ingredient.
getRelatedConceptsByRole (NDF-RT) to get the NDF-RT concepts that are related to the ingredient through the role "may_treat".

Creating the Workflow

To create the application, enter the RxMix web page. The figure below shows the initial RxMix page.

To define the workflow, click on the arrows at the right side of the box under "Select Function" and select "findRxcuiById".

The Optional Parameters labeled "id_string" and "flag" will appear. In the selection box for "id_string", select "NDC". The display should look like the image below.

Click the "Add to Workflow" button to enter this function into the workflow.

Next, select function "getRelatedbyType". The optional parameter labeled "term_type" will be displayed.

Select "IN" from the term_type menu.

Click the "Add to Workflow" button.

Next, select function "findConceptsByName" under the NDF-RT section on the menu. The optional parameter labeled "kind" will appear.

Select "DRUG_KIND" from the kind menu.

Click the "Add to Workflow" button to enter this function into the workflow.

To finish the workflow, select function "getRelatedConceptsByRole" from the menu. The optional parameters labeled "role_type" and "transitive" will be displayed.

Select "may_treat" from the role_type menu.

Click the "Add to Workflow" button to enter this function into the workflow.

Saving and Loading the Workflow

Click the "Save" button in the Execute section to save the workflow configuration. A popup menu will prompt you to save the file.

To test loading the workflow configuration, click the "Clear" button to delete the workflow from the RxMix page.

In the workflow section, click the "LOAD CONFIGURATION" button and select the workflow configuration that was just saved. The workflow should look like the figure below.

Note: The parameters for each function can be viewed by moving the cursor over the function name in the workflow graph.

Selecting Output Options

RxMix allows filtering of the output variables produced by the last function of the workflow. RxMix also lets the user choose which format to display the output - XML, JSON, TEXT or TABLE.

Uncheck the kind box in the Output Filter section.

Select the TEXT item under the Output Format section.

Create an Input File

In a text editor, create an input file with the following NDC values (one per line):

00591377510
00781318273
00093577001

Save the file. This will be used as input to the workflow.

Creating a Batch Job

To create a batch run in RxMix, click on the "Run Batch" tab in the Input section. The Batch Form will be displayed.

Enter your email address and the file name of the input file previously created.

Click on the "Submit" button to start the batch processing. An email message will be sent to you with a link to the results of the run.

The text results should look like this:

F0|findRxcuiById|I0|00591377510|F1|getRelatedByType|I1|617310|F2|findConceptsByName|I2|atorvastatin|F3|getRelatedConceptsByRole|I3|N0000022046|name|Arteriosclerosis|NUI|N0000000473
F0|findRxcuiById|I0|00591377510|F1|getRelatedByType|I1|617310|F2|findConceptsByName|I2|atorvastatin|F3|getRelatedConceptsByRole|I3|N0000022046|name|Coronary Artery Disease|NUI|N0000000856
F0|findRxcuiById|I0|00591377510|F1|getRelatedByType|I1|617310|F2|findConceptsByName|I2|atorvastatin|F3|getRelatedConceptsByRole|I3|N0000022046|name|Hypercholesterolemia|NUI|N0000001580
F0|findRxcuiById|I0|00591377510|F1|getRelatedByType|I1|617310|F2|findConceptsByName|I2|atorvastatin|F3|getRelatedConceptsByRole|I3|N0000022046|name|Hyperlipidemias|NUI|N0000001592
F0|findRxcuiById|I0|00591377510|F1|getRelatedByType|I1|617310|F2|findConceptsByName|I2|atorvastatin|F3|getRelatedConceptsByRole|I3|N0000022046|name|Hyperlipoproteinemias|NUI|N0000001594
F0|findRxcuiById|I0|00591377510|F1|getRelatedByType|I1|617310|F2|findConceptsByName|I2|atorvastatin|F3|getRelatedConceptsByRole|I3|N0000022046|name|Hypertriglyceridemia|NUI|N0000003210
F0|findRxcuiById|I0|00781318273|F1|getRelatedByType|I1|310414|F2|findConceptsByName|I2|fomepizole|F3|getRelatedConceptsByRole|I3|N0000148539|name|Drug Toxicity|NUI|N0000001000
F0|findRxcuiById|I0|00093577001|F1|getRelatedByType|I1|314154|F2|findConceptsByName|I2|olanzapine|F3|getRelatedConceptsByRole|I3|N0000148465|name|Bipolar Disorder|NUI|N0000000553
F0|findRxcuiById|I0|00093577001|F1|getRelatedByType|I1|314154|F2|findConceptsByName|I2|olanzapine|F3|getRelatedConceptsByRole|I3|N0000148465|name|Psychotic Disorders|NUI|N0000002532
F0|findRxcuiById|I0|00093577001|F1|getRelatedByType|I1|314154|F2|findConceptsByName|I2|olanzapine|F3|getRelatedConceptsByRole|I3|N0000148465|name|Schizophrenia|NUI|N0000002690

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