HERON (Healthcare Enterprise Repository for Ontological Narration) is a search discovery tool that allows you to search de-identified data from various hospital and medical center sources that include but are not limited to Epic/O2 (the hospital electronic medical record), IDX (the clinical billing system), KU Hospital Cancer Registry, REDCap (selected projects), Social Security Death Index, and University HealthSystem Consortium (Quality Measure Data). By combining the various data sources, researchers can look at the data in new ways not available when viewing data from one source at a time.
HERON Sponsorship Process
Qualified faculty can sponsor collaborators and research team members:
- Visit
1.Note: If you are outside the KUMC network, you will need to use a KUMC VPN connection.
- Log in with your regular KUMC login/password, just as you would use to access my.kumc.edu
- Follow the HERON Sponsorship Request link
1.Note: This link is only visible to faculty members.
- Enter the ID(s) for your sponsoree(s) and add
- The form should autofill your information and the sponsoree(s) information, Make sure the following fields are complete.
- Sponsoring faculty member full name
- Sponsoring faculty member network ID
- Title of research area for candidate
- Research expiration date (if applicable)
- Select "Sponsorship"
- Read the "Sponsor HERON System Usage Users" agreement. You will acknowledge agreement to the terms listed upon submission of the form
- Provide a description of candidate activities with regard to HERON usage
- Attach files (optional)
- Candidate KUMC network ID
- Candidate name, title, and department
- If the candidate is not a KUMC employee, please enter affiliation
Note: Candidate must have a network ID to access HERON even if not employed by KUMC
Submit the application. The system will notify the Data Request Oversight Committee (DROC) by email that an application is pending approval. In a few days, you should get notice of approval (or otherwise) by email.
If the request is approved, the candidate will receive an email as well; they can execute the
system access agreement and log in to HERON as usual.
Create a search
- Search by dragging and dropping concepts (e.g., search terms) into groups
Search options include:
- Limit by dates
- Searching within the same financial encounter
- Defining multiple occurrences
- Excluding items, and more
Obtain a Data Set
Each tool requires a patient set, also called a patient list. To create a patient set, click the Patient List checkbox on the search pop-up that appears after you click Run Query. Once the search is complete, you can access the patient set in the previous query box (lower left section of the screen) by clicking on the search title and opening the results folder.
- Demographics - quickly create a bar graph for demographic information (e.g., gender, race, etc.) for one or two patient sets.
- Timeline - create a visual representation for patient observation occurrence. Observations are marked with a tic on a timeline. Hover over the observation tic for additional information, such as time or value when available.
Request Data
Receiving Data
- After a data request has been approved by the Data Request Oversight Committee (DROC) a HERON team member will provide you with the data. You will receive a REDCap project and the raw data. The raw data will be attached in the file repository of the REDCap project or sent via KUMC's securefiles.
Steps to obtain a data set:
HeronDataSet explains the structure and format of the data set.
Search
- Start the i2b2 Query & Analysis Tool. Conduct desired query. For general help on how to conduct a search, click on the "Help" link located in the upper right portion of the i2b2 Query & Analysis Tool.
- Enter a search name of your choice, and make sure to check the "patient list" checkbox. Always give an appropriate name for future reference to the query and store it in your folder (it has your name) in the Workplace area.
- After search results are returned, move the search from the Previous Queries area to your folder (it has your name) located under the "Shared Folder" in the Workplace area.
- Once saved, if you think that is the query that you want to use as a result, move the query into the shared folder in the Workplace area by dragging and dropping the search into the shared folder.
How to request a data set
NOTE:
Faculty members with access to HERON may request a de-identified or identified data set that can be downloaded into programs such as Excel, SPSS, or SAS.
Non-faculty researchers will need to have a sponsorship request submitted and approved by a faculty member.
Requests to access data can be granted after the user:
- Submits a description of the project.
- Names of study team members.
Note:
-
De-identified data requests do not require HSC approval.
- Identified data requests require prior IRB approval from HSC.
Note: Contact information from potential research participants in the
Frontiers and Pioneers Participant Registry can be requested.
Submit Request
- Visit https://heron.kumc.edu using any web browser.
Note: If you are outside the KUMC network, you will need to use a KUMC VPN connection.
- Log in with your regular KUMC login/password just as you would to access my.kumc.edu.
- Select the "HERON Data Usage" link to access and complete the following form.
- For Identified data request - HSC/IRB number and an attached IRB Protocol are required.
- List all individuals who need access to the data on the request.
- Submit upon completion of the form. The system will notify the Data Request Oversight Committee (DROC) by email that a data request is pending approval. Within a week, you should receive notice of approval (or otherwise) by email. The i2b2 team will provide you with access to the requested data set.
Questions?
Contact the Data Concierge dataconcierge@kumc.edu or call x8-7205.
Receiving HERON Data
After a data request has been approved by the Data Request Oversight Committee (DROC) a HERON team member will provide you with the data. You will receive a REDCap project and the raw data. The raw data will be attached in the file repository of the REDCap project or sent via KUMC's securefiles.
Understanding the REDCap Project:
- There is one record per patient in the query.
- Each concept (i.e., lab value, diagnosis, etc.) has the first recorded date and the last recorded date. For concept with numeric values (such as lab results), the REDCap project will also contain the first and last value.
1.To look at specific values, such as BMI 1 month before or 1 month after a surgery date, you will need to access the raw data found in the file repository.
- The "Stats and Charts" feature of REDCap can be very helpful to look at things such as demographics.
1.Be cautious when looking at lab values in "stats and charts," because it only takes into account the values uploaded into REDCap, not all of the values.
Understanding the raw data:
- Four CSV files are contained within the zip file: patient table, variable table, data table, and a code info table.
- The patient table contains one row per patient and includes basic demographic data.
- The variable table has one record for each of the i2b2 concepts you requested.
- The data table is in a long-skinny format containing multiple rows per patient. For example, if Vitamin D was requested in your search, patient 123 could have 30 rows just of Vitamin D levels (1 row per lab result).
- The code info table has information about the codes requested in the HERON query
- More information regarding what is contained in each CSV file is found here.
- Raw data can be transformed using SQLite in preparation for analysis in a statistical software.
- Instructions to upload de-identified data into SQLite using sql-schema.sql
- Instructions to upload identified data into SQLite using dataset_import_identified.db
Upload HERON Data into SQLite
Learning SQL Training Videos:
**Please note all data are fabricated in the following examples. The code written in the videos is found starting on page 24 of the HERON training manual.
Transform HERON data with SQL-1
Transform HERON data with SQL-2
SQL using date windows-HERON Data
Transform HERON Data Using SQL-Y
HERON Data Transformation- Join All
Access HERON from a secure KUMC network or via the KUMC VPN at https://heron.kumc.edu
Need help? Watch our HERON Training Videos or see below for frequently asked questions.
What is HERON?
HERON (Healthcare Enterprise Repository for Ontological Narration) is a search discovery tool that allows you to search de-identified data from various hospital and medical center sources that include but are not limited to Epic/O2 (the hospital electronic medical record), IDX (the clinical billing system), KU Hospital Cancer Registry, REDCap (selected projects), Social Security Death Index, and University HealthSystem Consortium (Quality Measure Data). By combining the various data sources, researchers can look at the data in new ways not available when viewing data in one source at a time.
asked questions.
Why should I use HERON?
HERON is a powerful tool that can save time during your research process. Searching across multiple data resources allows you to view data trends, key in on your research criteria, and modify your search requirements and see how the data changes. This is a good tool to employ at the start of a research project as it saves time by helping you focus and define your research. The HERON tool also provides analysis tools, such as the Timeline and the Cancer Survival Analysis tools.
asked questions.
How do I access HERON?
Three criteria need to be met before you obtain view-only access to do patient count queries:
- You are a qualified faculty member or are sponsored by a faculty member. Access to de-identified data is non-human subjects research and does not require approval by the HSC/IRB.
- You are up-to-date on your
Human Subjects Training.
- You sign the system access agreement
NOTE:Not sure if you meet these criteria?
-
Contact our Data Concierge at dataconcierge@kumc.edu OR
-
Log onto https://heron.kumc.edu. Look at the upper left corner of the screen. All 3 check-boxes should be checked. Any missing checks indicate a requirement not met.
Need to be sponsored? Here are instructions on sponsorship
or a training video
for a faculty member to sponsor you.
Can I access HERON off-campus?
HERON is available from the KUMC network. If you are working outside the KUMC network, you will need to use a KUMC VPN connection. KUMC VPN is available to University faculty, staff, and UKP employees. Sponsored students have to access HERON from a KUMC network.
How do I search HERON?
HERON allows you to browse or search for concepts and easily drag and drop into groups to create a search.
Video: Perform a simple search
https://www.youtube.com/watch?v=yt7djtOkk-0
Video: Tool interface overview
https://www.youtube.com/watch?feature=player_embedded&v=1GroXZA_iTo
What data is in HERON?
HERON integrates data from local clinical systems (clinical systems such as EPIC and IDX), University systems (REDCap, Cystic Fibrosis Registry, Tumor Registry), and national systems (Social Security Death Index).
When creating your search, it is important to understand where the data comes from as well as the time limits for each type of data. For example, do not search Flowsheet data targeting events in 1975 as it is not available in HERON.
How is the data de-identified?
HERON does not include any identifying information, such as a Medical Record Number (MRN), name, address, or birth date. In an effort to further de-identify the data, we shift dates to a random date within 365 days prior to the actual date. The same random time shift is applied to all events for that patient. For example, a patient named Birdy was born on 1/1/1950 and was diagnosed with asthma on 4/1/1965. HERON randomly shifts Birdy's birth date 60 days to 11/3/1949 which means the asthma diagnosis date is also shifted 60 days to 2/1/1965. HERON also de-identifies a patient's location by limiting searches to a distance from KUMC as opposed to searching a specific zip code.
Can I get more than just the number of patients that meet my search criteria?
Faculty members can submit a request for de-identified or identified data. The request will be reviewed by a committee comprised of members from KUMC, KUH, and KUP. Turn-around time on requests vary but generally expect 1-2 weeks for approval and receipt of data set. See instructions for requesting a data set or watch the training video.
How do I get a list of patients I can contact who meet my research criteria?
You can search in HERON to see if patients consenting to be in a research study meet your research criteria. Create a search for the criteria needed in HRON (e.g., females over the age of 55 with diabetes and migraines). Limit your search with the Frontiers Research Participant Registry concept and exclude those patients deceased by dragging the deceased concept from demographics in a group. Once your search is complete, submit a Frontiers Research Participant Registry request. Please note that the Frontiers Research Participant Registry is only available to KUMC faculty.
Learn more about how to search HERON to find patients who are eligible for your research and who have provided consent to be contacted for research through the Frontiers Research Participant Registry.
Download HERON Manual
| Section |
Pages |
| General HERON Information |
4 |
| Logging into HERON |
5 |
| Hierarchical Structure |
6 |
| Running a Query / User Interface |
7-9 |
| Searching Techniques |
10-13 |
| Finalizing Queries |
14 |
| Requesting Data |
15 |
| Receiving Data |
16-21 |
| Uploading Data into SQLite |
22 |
| Basic Data Manipulation Techniques in SQL |
23-27 |
| Data in HERON |
28-37 |
- Simple Search
Introduction on creating and executing a simple search. Video demonstrates browsing and searching for terms in addition to placing concepts into groups for searching. Target audience: all HERON users.
- HERON Interface Overview
Introduction to functionality available in the HERON interface including options to focus or expand your search. Target audience: all HERON users.
- Searching by Codes
Introduction to using the search by code function to find diagnoses and procedures. Target audience: all HERON users.
- Timeline and Demographic Tool
Learn to use the timeline and demographic analysis tools. Target audience: all HERON users.
- Age vs. Age at Visit
Learn the difference between "age" and "age at visit". Target audience: all HERON users.
- ED Visits
Learn how to find patients who have been seen in the emergency department. Target audience: all HERON users.
- Medication Modifiers
Learn about medication modifiers and how to use them to limit your search. Target audience: all HERON users.
- Define Sequence of Events
Learn to use the define sequence of events function in HERON. Target audience: all HERON users.
- "Shopping Cart"
Learn to create a "shopping cart" which can contain all of the variables you are interested in analyzing and receiving in your data set. Target audience: all HERON users.
- Demographic Folder
Learn to navigate the demographic folder. Target audience: all HERON users.
- Same Financial Encounter vs. Independent Searching
Introduction to independent search constraint and the same financial encounter constraint. Target audience: all HERON users.
- Video Timing Out / Previous Queries
Learn how to find previous queries and what to do when the queries time out. Target audience: all HERON users.
- Shared Folder
Learn how to share queries with other HERON users. Target audience: all HERON users.
- Questions?
Contact the Data Concierge dataconcierge@kumc.edu
Frontiers and Pioneers Participant Registries Requests
The Pioneers Research Participant Registries include patients who have given permission to be contacted for future research studies. Pioneers Health System patients have all been seen at KU Hospital, whereas Pioneers Community patients are those in the community who may or may not have been seen at KU Hospital. Qualified researchers with IRB-approved protocols can use these recruitment tools to obtain contact information for individuals who match the criteria for their studies.
Requesting Patient Contact Information:
Requests for contact information are made to the Recruitment Registry Review Committee (RRRC), a multi-disciplinary committee with representation from the University of Kansas Medical Center, KU Hospital, and the University of Kansas Physicians, Inc. The RRRC screens for overutilization of population groups and individuals. Requests for identification of vulnerable populations are given special consideration.
To obtain patient contact information, please proceed to the heron homepage and complete the HERON Data Use or Recruitment Request form which is found on the left-hand side under Regulatory Requests.
Once approved, you will receive an approval notification and contact information will be sent separately in a password-protected file through Secure Filde Transfer. The file will be available for 30 days. It is recommended that you remind patients that they signed an authorization form in one of the outpatient clinics giving permission to be contacted in the future about research and that is why they are now being called.
An updated database search can be conducted every 3 months if requested. Please contact heron-admin@kumc.edu for more information.
Please note that the Pioneers Research Participant Registry is available to KUMC faculty or those with a KUMC co-investigator.
How to search HERON for Pioneers participants
- Start the i2b2 Query & Analysis Tool. Conduct desired query. For general help on how to conduct a search, click on the "Help" link located in the upper right portion of the i2b2 Query & Analysis Tool.
- Add Pioneers Research Participant Registry to a group and exclude Deceased in another group by clicking on the exclude link. This will limit the search to only non-deceased participants in HERON who have consented to be part of the registry.
-
- Enter a search name of your choice, and make sure to check the "patient list" checkbox. Always give an appropriate name for future reference to the query and store it in your folder (it has your name) in the Workplace area. Move the query to the shared folder when ready to submit request to the DROC.
- Complete Pioneers Research Participant Registry form.
Pioneers Website:
- Members of the community may register and consent to become a Pioneer.
- KUMC studies posted on clinicaltrials.gov are automatically posted on the website under Active Studies.
- Researchers can complete this form to request to post a study on the website.
- Researchers can request a basic study interest form to be added to the study listing.
- A button "I am Interested" will be shown on the study page. If patients click that they are interested, researchers will be given their contact information
- Fill out this form
Research Recruitment Video:
HERON for Research Recruitment
Integrate REDCap Projects into HERON
How to prepare your REDCap project to be loaded into HERON
Integration of REDCap project data into HERON is driven by our desire to empower the researcher to:
- look at a richer data picture of their project population.
- look for disparaties in data in the EMR versus the data in REDCap projects.
Since July 2012, REDCap projects that model breast cancer, Alzheimer's, Sepsis management registries among others have been integrated into HERON. Below, we briefly summarize how you can get your REDCap project ready for integration into HERON.
- Make sure you document the MRN for patients in your project
- REDCap data related to a patient is linked to the rest of their EMR data using their Medical Record Number (MRN). Please make sure you record the MRN accurately for the patients with all the leading zeros. Patients missing valid MRN will not be loaded into HERON.
- Verify that no two records in your REDCap project have the same MRN
- If two records (i.e. patients) have the same MRN, then your REDCap project should be modeled as a longitudinal project. If you have questions regarding longitudinal projects, please watch the relevant video. If you need further
- Mark the fields containing PHI as "Identifiers"
- If you are recording PHI in a field in your REDCap project, please make sure you have marked that field as an identifier. You can do that from an online designer. Once a field has been marked as an identifier the data in it will not be loaded into HERON so that we can comply with our "de-identified data only" policy.
- Check the REDCap field types in your project
- Right now we only pull the following REDCap field types into HERON:
- Text fields with integer, float, or data validation. We ignore text fields without any validation.
- Radio, checkbox, select (dropdown), yes/no fields.
- Make sure the data you want to look at in HERON is in those fields. If not, please contact us and we can try to expand this list. We do not load data from unvalidated text fields due to the de-identification challenges.
- Verify the user rights to your project
-
Currently, access to your REDCap data in HERON is limited to only users who have permission to it in REDCap.
- Project Status: Production
-
Finally, make sure your project has been moved to Production. This is a good practice for REDCap projects as it helps protect the project structure and data against inadvertent changes.
- Our releases are around the middle of the month
-
For your project to be part of the next monthly release, the project has to be ready by the first week of a month. We will first stage the data and will contact you if we have any obvious issues that we need your help in resolving.
- Request to integrate your project
-
Please complete the REDCap-to-HERON Request so that we can integrate your project into HERON. Choose options HERON and then REDCap to HERON Request.
- Contact us
If you have any questions contact us at: misupport@kumc.edu
Understanding Free-Text Notes in HERON
Free-Text Notes
A new feature in HERON is the ability to request de-identified free-text notes. These notes include physician and nursing notes, radiology, and pathology reports. Prior to bringing in a note type, the notes are de-identified. There are two steps in our de-identification framework: notes de-identification and notes adjudication. The notes de-identification step removes all identifiable information such as names of patients, locations, identification numbers, dates, and age above 90 in order to meet HIPAA Safe Harbor criteria. During notes adjudication, notes are audited to ensure PHI removal and the note de-identification performance was evaluated before releasing.
We offer Natural Language Processing (NLP) support for information extraction from the free-text clinical notes on a project basis (funding required). Please contact misupport@kumc.edu for inquiry.
Available de-identified note types in HERON include:
- ED Notes
- Initial Assessments
- OR Nursing
- Committee Review
- Discharge Inst - Activity
- Discharge Inst - Diet
- Discharge Inst - Appointments
- Discharge Inst - Other Info
- DIscharge Inst - Signs / Symptoms
- Discharge Inst - Case Management
- Discharge Instructions
- Nursing Note
- Pre-Anesthesia Patient Instructions
- Critical Results
- Operative Report (DICTATED ONLY)
- Op Note
- Brief Op Note
- Rehab Team Physician
- Procedures (Immed Post or Bedside)
- Pathology
- Radiology
GREEN HERON
As part of the KU Medical Center CTSA Informatics Core, we aim to streamline research processes by providing clinical data analysis environments and to engage investigators in the use of informatics tools for collaboration across the entire spectrum of translational research. KU Medical Center has established an integrated clinical data repository, HERON, with approximately 2 million patient electronic medical records (EMR) as well as research participant registry, socioeconomic data, and death data, which is a valuable resource for clinical and translational research. To engage the broader scientific community and catalyze research collaboration, we have expanded HERON's capability by creating an open and protected clinical data analytic environment called Green HERON.
Green HERON is a secure health data analytic space where approved users can work with de-identified health information. Green HERON simplifies the effort of obtaining EMR data from HERON, while supporting collaborators from partner institutions with approved NetIDs. The analytics space offers a rich set of tools, services, and resources required by research. Within the protected environment, Green HERON users are provided the ability to select analytic tools such as R, SAS, and Python.
Requirement for access:
- Secure KUMC network (either on campus or via VPN)
- KUMC Faculty member or sponsored by a faculty member
- Up-to-date Human Subjects Training
- Signed system access agreement
*KUMC affiliated accounts can be created upon request and institutional approval
Software tools available:
- SQL Developer
- R and RStudio
- Python
- STATA
- SAS
*Additional software can be installed upon request and approval.
Contact Information
For assistance with research data needs/project development contact our dataconcierge@kumc.edu
For HERON and REDCap support by email: Contact MI Support at misupport@kumc.edu
Location:
University of Kansas Medical Center
Office of the Chief Research Informatics Officer
Student Center, 3001C,
3901 Rainbow Boulevard
Kansas City KS 66160
913-588-7251
