Chiron User Guide
- Karen Lapthorn
The Data Catalog User Guide provides detailed instructions on the primary features and functionality of the Chiron Data Catalog websites.
Table of Contents:
Help and Resources
If you need additional help or training using the RData Catalog, need to report an error, or have a question, use the RDCRN Service Desk to contact us.
How to access the RDCRN Data Catalog websites
RDCRN Consortium Chiron
The RDCRN Consortium Chiron can be access by RDCRN members only. Access to view individual data sets must be requested and granted by a member of the DMCC Chiron Administration team. Requests can be submitted via the RDCRN Service Desk.
RDCRN Consortium Chiron can be accessed using RDCRN credentials via the url: https://datacatalog.rarediseasesnetwork.org/.
Public Chiron
A separate Chiron website allows for non RDCRN members to log in and view Aggregate only data for select RDCRN data sets. No subject-level data is available to view in the Public Chiron website.
Public Chiron can be accessed via the url:
https://publicdatacatalog.rarediseasesnetwork.org/
Users need to login, but they do not need to be RDCRN members. They can use their existing institutional credentials or a Login.gov account.
Permission Levels
Each data set within Chiron has its own set of users and permissions. A user can be given access to
Aggregate data only
Subject-level, de-identified data
Full data access including fields flagged as PHI (example: visit dates)
Select a Dataset
After logging in to access Chiron, you will see a list of all Datasets. The datasets you have access to will display a ‘VIEW DATASET’ link.
Dataset Homepage
After selecting to view a dataset, the dataset homepage will display. This page will show details about the dataset including the date of last import, total number of subjects and your access level.
Query Tool
Accessing the Query link from the top menu give you a list of all variables that have been transferred to Chiron from the data source (such as REDCap).
Browse Data
Use the left column to browse variables (called “Concepts” in Chiron) which grouped into sections such as Enrollment, Visit, Medical History, etc. Expand each category and click on a variable name to view charts or lists representing the records.
Concepts with a lock icon have been flagged as PHI in the Chiron database and will be hidden from users who can view only de-identified data.
Use the Search Concepts box at the top of the list to quickly find a specific concept.
Build a Simple Cohort
By default, the Subject Count will display all Subjects in the dataset. You can use use concepts to filter the Subjects to a desired cohort.
To build a cohort, select the desired variable(s) and click the ‘Apply New Filter’ button. You will see your cohort definition and corresponding Subject Count in the right column.
▶ Video Example: Create a simple cohort
This example shows how to create cohort of only Female subjects.
Select Gender from the list of concepts
Select the checkbox next to the entries labeled as female
Click Apply New filter button
Total Subject Count value is reduced to just the number of subjects in the new cohort
Once you have built a simple cohort, you may Select additional concepts to further refine the cohort. You can add as many concepts as you wish and the filter details will update in the right column.
Exclude Filter option
Use the Exclude Filter option to refine the cohort. Select the value(s) to be excluded, toggle ‘Exclude Filter’ and Apply.
Example:
Show data for active cohort only
Enabling the Show data for active cohort only toggle changes the data shown for each concept to only display data for the defined cohort. When this is enabled, you can browse each concept and see data for the current cohort only. When this toggle is not enabled, the data shown for each concept will reflect the entire subject population.
Create a temporal query using longitudinal data
Datasets containing longitudinal data support the creation of temporal or event-based cohorts. Examples filters include:
Subjects who received drug X within 3 months of stem cell transplant and who have brain MRI post transplant.
Subjects who scored over X on a clinical rating scale after receiving XYZ treatment at an encounter.
Results View
Use the Results menu item to view of subject-level data. The records shown will include all subjects included in the cohort defined in the Query Tool. Or, clear cohort criteria in the left column to view records for all subjects.
Define Columns
Including the subject Record ID as a column is often the best place to start and this column is included by default. Next, use the Edit Columns link to select additional concepts to include as columns in your Results view. Here you can also remove and reorder columns.
▶ Video Example: Add columns of data in Results View
Aggregation Method for Columns
Use the pencil icon at the top of each column to see a menu with a number of options for how to display multiple values for the selected concept.
Stack (one row per data point)
If a single subject has more than one value for the concept, multiple rows will display for the subject.
List Distinct
If a single subject has more than one value for the concept, all distinct values will be listed in a single row separated by a semi colon. No repeated values will be listed.
List All
If a single subject has more than one value for the concept, all values will be listed in a single row separated by a semi colon. Repeated values will be listed.
Count Distinct
If a single subject has more than one value for the concept, a count of distinct values will be displayed.
Count All
If a single subject has more than one value for the concept, a count of all values will be displayed.
Most Frequent Value
If a single subject has more than one value for the concept, only the most frequent value (or 2nd most frequent, or 3rd most frequent…) will be displayed. Additional options can be set to display the count or both the count and the value.
Latest Value
If a single subject has more than one value for the concept, only the latest value (or 2nd latest value, or 3rd latest value…) added will be displayed.
Earliest Value
If a single subject has more than one value for the concept, only the earliest value (or 2nd earliest value, or 3rd earliest value…) added will be displayed.
Has Value
If a single subject has more than one value for the concept, you can display True/False for specific values. You can also choose to display a count for specific values.
Aggregation Methods Examples
Below are some screenshots showing examples of aggregation methods using 2 columns of data:
Patient ID: Aggregation Method on this column is always set to ‘Stack’
Medication Code: numeric codes that represent Medications that the patient has indicated they are taking over the course of the study
The screenshot shows the result of applying each aggregation method to the Medication Code column.
Aggregation Method | Result |
|---|---|
List All: for each Patient ID, all Medication Codes, including duplicates, are listed in a single row separated by a semi colon. | |
List Distinct: for each Patient ID, distinct Medication Codes are listed in a single row separated by a semi colon. Unlike with List All, each patient’s duplicate codes have been removed. |
|
Stack: Each Medication code is listed one per row. If a patient has more than one Medication Code, their Patient ID can be seen listed multiple times in the Patient ID column. | |
Count Distinct: Instead of displaying the Medication Code values for a patient, show the count of unique codes for each patient. |
|
Count All: Instead of displaying the Medication Code values for a patient, show the count of all codes (including duplicates) for each patient. |
|
Most Frequent Value: Display only the most frequent Medication Code that is associated with each patient. |
|
Save Query as Report
Save your Results View as a Report by using the Save Query button. The report will save both your selected columns of data and any cohort filters.
When saving a Report you will see the following options:
Choose to Create a new Report or Overwrite an Existing Report.
Give the Report a Name.
Organize the Report into an existing Project or create a new Project. Projects can be thought of as categories or folders that house Reports. You can have one or many Projects.
Give the Report a Description (optional)
Select who can view the report:
Leave the Share options blank to keep the Report private and viewable only by you.
Select one or more users who also have access to the data set in Chiron.
Or, select to share with everyone who also has access to the data set in Chiron.
If the report is shared with others, it cannot be changed or deleted by anyone but you. Others can load a copy of your report into the Results view, make changes and save as a new Report.
Download CSV
Use the Download CSV option to export the Results view columns and rows.
Reports
Reports saved from within the Results View are kept in the Reports section of the site. Reports can be shared with other users who have permissions to access the same data set within the Data Catalog.
Quick Guide to Building a Report
First use the Query View to define a cohort. Or, skip this step to include all subjects in the cohort.
Next, use the Results View to select the data to include in the Report. Add columns of data and set the desired Aggregation Method on each column.
Save the Report and select who can view the report.
Load a Report into Results View
Use the Load Into Workspace link to load a saved Report into the Results view. You can then make updates to the filters as well as the columns. Once you have made changes, you can overwrite the original Report or save your changes as a new Report.
Download a Report
Reports can be downloaded using the Download CSV button in the Reports section, or after the Report is loaded into Results View.
Aggregate View
The Aggregate View tool allows you to display data in tables showing subject counts. No subject-level data can be viewed in the Aggregate View.
Use the Edit Columns and Edit Rows links to build your table. Select a concept from the list (or use the Search box to locate a concept). Click Update to view the aggregate counts for the selected concepts in table format.
▶ Video Example: Create an Aggregate table
This short video shows how to build a simple aggregate table where I can view subject Conditions by Gender. I have already used the Query view to set a cohort of only subjects who have an Ethnicity set to “nonhispanic.”
Additional options allow you to easily Swap Rows & Columns in the Aggregate table as well as Clear all selected concepts. You can also download a csv file containing the data shown in the table.