A Step By Step Guide to Self Service Chart Review

Step 1 - Research Compliance and Privacy Approvals

In order to create a list of patients (also known as a "cohort" of patients) for online chart review, you need to have contacted the Stanford Research Compliance Office.

     Prep to Research: If you are still in the preparatory to research phase, you can provision yourself a chart review up to 50 de-identified charts, available for 90 days.
     Research: If your intent is research, you must have an approved IRB protocol.
     Clinical QI: If your intent is not research, you must obtain a determination of Non Human Subjects (NHS) from the Research Compliance Office in order to use this self-service tool.

Everyone on the research team must individually attest that they are wiling to assume and honor the data privacy obligations that come with working with clinical data for research. If your IRB already has a primary DPA completed by someone else on the team, you must add your attestation to the existing approved primary attestation as described on our Add-On Privacy Attestation page.

Step 2 - Cohort Definition

After you have your compliance matters settled, the next step is taken in the Cohort Discovery Tool.

Before you can review patient charts online for research purposes, you must first specify which patients whose charts you wish to review.

You can rapidly build an ad hoc patient phenotype definition using the Cohort Discovery Tool to characterize the patients of interest. Drag suitable search constraints from the left hand toolbox into the query builder on the right. Detailed instructions are available in the Cohort Discovery Tool Users' Guide. Once you have a suitable search query defined, select "Save for Chart Review" from the dropdown menu under the "Counts" toolbar button in the upper right.

Alternately, if you have a list of MRNs, e.g. from a research database such as REDCap, you can use it to specify your patient list for chart review by selecting "Upload MRNs for Chart Review" from the Cohort Discovery Tool using the dropdown menu under the "Counts" toolbar button in the upper right.

Please note that for cohorts with more than 7,500 patients we limit the size of chart review cohorts to the first 200 patients. If you wish to review more than 200 patients in a very large cohort, please break it up into chunks smaller than 7500 each.

Step 3 - Name Your Cohort and Specify IRB, PHI, and Collaborators

When you save your list, you will see a dialog box prompting you for

  1. the cohort name 
  2. your IRB or DPA number
  3. what PHI is minimally necessary, and the date masking approach should you choose to scrub dates
  4. whether you wish to include death data from the Social Security Administration, and
  5. who else will be assisting you with the chart review

If you leave "Scrub PHI (best-effort)" checked, your cohort will be scrubbed of identifying information to the extent possible. This can be very handy e.g. when students are helping with chart review, as it does allow them to work with the minimum necessary PHI.

When you complete filling in the form and click "Create Cohort", you will be prompted to either continue searching for cohorts or switch to chart review.

To switch to chart review, you have the option of either clicking the toolbar button "Go to Chart Review", or selecting "Patient Chart Review" from the dropdown menu in the application header above the toolbar.

If you already have charts to review, in order to get the newly created cohort to appear in your list of cohorts you may have to refresh your browser window.

For other troubleshooting tips at this stage or any other part of the process, please refer to our Frequently Asked Questions page.

Step 4 - Read the User's Guide

It is well worth the effort to scan through the Chart Review Tool User Guide, as it describes several time-saving features that are worth knowing about.

Step 5 - Review Charts, Flagging as you go

As described in the Users's Guide, you can tag patients who do and do not meet your inclusion criteria. You can then use these tags to filter data for download.

Step 6 - Download your data

Some research projects can benefit from a data download. Use the "Create Download Files" button in the upper right to generate. Note that particularly for large cohorts the download file generation process can take a long time. When complete, a list of available files will appear in the upper right.  Downloads are limited to 7500 patients; if you have a need to download more than this number, please get in touch with the Research Informatics Center to remove this limit for your cohort.

Please also note that as of June 2023, by policy all downloaded data is scrubbed of PHI using our best-effort techniques. If your research requires PHI in downloaded data files, you may apply for a personal, non-transferable exemption to this policy.

If you are expecting to see the option to download PHI but it is not appearing, click on the blue infobutton after the statement "These files will be scrubbed of PHI. More Info:". The full list of missing requirements will then be displayed as a popup.

Further Information

Please consult our FAQ if you have any further questions.