Phenotyping a dataset
Phenotyping involves computing selected phenotypes in a selected dataset, and performing an action on the computed phenotypes and the selected data. To get started, select Jobs in the main menu bar.
Select a data source
Your Eureka! deployment’s administrator is responsible for configuring your user account to access the data sources you need. Data sources may be an Excel spreadsheet or another dataset or database that your administrator has configured. When you select a data source from the dropdown list, form fields may appear for you to complete, such as the name of a spreadsheet file on your local computer. Required form fields are marked by an asterisk.
Select an action
Actions will phenotype the dataset and output it. Again, your Eureka! deployment’s administrator is responsible for configuring the actions to which your user account has access.
Specify the data to process
The same concept browser as in the phenotype editing screens is available in the jobs screen. Select the System tab in the concept browser. Drag concepts corresponding to the data to want to process (patients, encounters, labs, meds, etc.) into the Concepts box.
Specify the phenotypes you want to compute
The same concept browser as in the phenotype editing screens is available in the jobs screen. Select the User tab in the concept browser, and drag any phenotypes that you want to compute into the Concepts box. If you select no phenotypes, the system will omit phenotyping and just perform the selected action on the selected data.
Specify a date range
Specifying a date range is optional. If you do not specify one, the entire dataset from the selected data source will be phenotyped and output. The same concept browser as in the phenotype editing screens appears in the jobs screen for you to select a data element to which to apply a date range. Drag the selected element into the blue box. Then, specify your date range of interest using the form fields.
Start a phenotyping job
Click Start to begin a job. The job’s status will be updated at the top of the screen. You may leave this screen or even logout of Eureka!, and the job will continue running in the background. When the job is complete, a link will appear in the job status area that will take you to a tool for browsing the phenotypes and data that have been processed.