HERON Council Grove update includes histories, encounter vitals and expanded smart notes
The Council Grove release introduces family and social histories within the HERON tool. Family history can be searched by all or by a particular family member type (e.g., Maternal Grandmother). Additionally, a new modifier allows searching by medical history within the clinical diagnosis folders. Other data changes within HERON include encounter vitals, which are searchable under the Visit Detail folder, and smart data notes, which are expanded to include ambulatory in addition to the previously released inpatient notes.
HERON Council Grove Contents Summary
This month, our tour of rivers and lakes in Kansas honors Council Grove Lake.
The HERON repository contains approximately 1 billion real observations from the hospital, clinics, and research systems:
Observation | Patients | Source | Go-Live | Snapshot | Issues | |
---|---|---|---|---|---|---|
Demographics | 18.5M | 1.95M | ||||
KUH Billing (O2 via SMS) | 1980s | Dec 2012 | various* | |||
UKP Billing | 2000 | Dec 2012 | ||||
15K | 15K | Frontiers participant registry | Jun 2009 | Dec 2012 | ||
187K | 187K | Social Security Death Index | 1962 | Dec 2012 | ||
Diagnoses (IDC9) | 42.4M | 657K | ||||
KUH/O2/Epic | Nov 2007 | Dec 2012 | various* | |||
UKP Billing | 2000 | Dec 2012 | ||||
University HealthSystem Consortium (UHC) | Q4 2008 | Sept 2012 | ||||
History | 10.9M | |||||
KUH/O2/Epic | Nov 2007 | Dec 2012 | ||||
Medications | 78.7M | 302K | ||||
KUH/O2/Epic (Organized by VA Class) | Nov 2007 | Dec 2012 | various* | |||
Nursing Observations | 563M | ? | ||||
KUH/O2/Epic | Nov 2007 | Dec 2012 | various* | |||
Lab Results | 83M | 289K | ||||
KUH/O2/Epic | 2003 | Dec 2012 | various* | |||
Procedure Orders | 113M | 441K | ||||
KUH/O2/Epic | 2003 (?) | Dec 2012 | various* | |||
Procedures (CPT) | 10.6M | 578K | ||||
UKP Billing | 2000 | Dec 2012 | ||||
Reports/Notes | 35.7M | 278K | ||||
KUH/O2/Epic | ? | Dec 2012 | ||||
Specimens | 44.3K | 3.79K | ||||
KUMC Biospecimen Repository | ? | Dec 2012 | ||||
Visit Details | 27M | 527K | ||||
KUH/O2/Epic | Nov 2007 | Dec 2012 | ||||
Cancer Cases | 9.8M | 66.4K | ||||
KUH Cancer Registry | 1950s | Dec 2012 | labels* | |||
Hospital Quality Metrics | 4.43M | 65.2K | ||||
University HealthSystem Consortium (UHC) | Q4 2008 | Sept 2012 | ||||
Triple Negative Breast Cancer Registry (BRCA) | 20.9K | 122 | ||||
REDCap | July 2011 | Dec 2012 | #1741 | |||
All | 1B |
Notice
Some material in the UMLS Metathesaurus is from copyrighted sources of the respective copyright holders. Users of the UMLS Metathesaurus are solely responsible for compliance with any copyright, patent or trademark restrictions and are referred to the copyright, patent or trademark notices appearing in the original sources, all of which are hereby incorporated by reference.
Beta Disclaimer
We are providing this early access to obtain feedback from you, the research community. While we are actively working on validating the data loaded into the system with hospital and clinic technical staff, there may be problems with our translation of data from our source systems (HospitalEpicSource and ClinicIdxSource) into HERON.
Please email us at heron-admin@kumc.edu if you discover information you believe may be erroneous.
We are actively working on enhancing the types of data included. Stay tuned to our roadmap to track progress toward upcoming releases.
Various Issues Still Apply
Keep in mind the issues noted in the original HERON beta notice, including:
- date shifting, part of our DeIdentificationStrategy
- age searching (#158)
Enhancements and Problems/Defects/Issues Addressed in this Release
- #178
- Query for encounter vitals in HERON
- #766
- Query for social history (e.g. tobacco use) in HERON
- #826
- some flowsheet observations are not connected to the relevant encounter
- #1515
- Query past medical and family history from Epic for ambulatory and inpatient
- #1516
- query smart data note concepts from the ambulatory environment
- #1655
- realistic date-of-death exposed details about ages > 90
Outstanding Problems/Defects/Issues
Ticket | Summary | Keywords |
---|---|---|
#2301 | constraining birth-date by date doesn't work - HERON uses sysdate for start_date in demographics | public-web wrong-results training |
#2617 | Saved searches not updated in REDCap projects after Arkansas release | public-web redcap-to-heron |
Quick-and-dirty usage documentation for python integration tests
In addition to my addiction to python's doctest for WritingQualityCode, I'm developing a habit of letting my modules serve as their own integration tests when run as scripts. Python comes batteries-included with argparse, and Aargh is pretty cool, but for quick-and-dirty stuff like this, I tend not to bother at all. I just let python's stack traces serve as documentation.
For example, if it's been a while since I used source:raven-j/heron_wsgi/admin_lib/i2b2pm.py, I just run it, and I get:
(haenv):admin_lib$ python i2b2pm.py Traceback (most recent call last): File "i2b2pm.py", line 319, in <module> _test_main() File "i2b2pm.py", line 289, in _test_main user_id, full_name = sys.argv[1:3] ValueError: need more than 0 values to unpack
The user_id, full_name = sys.argv[1:3]
line is typically enough of a clue to remind me what arguments are needed:
(haenv):admin_lib$ python i2b2pm.py dconnolly 'Dan Connolly' DEBUG:__main__:generate authorization for: ('dconnolly', 'Dan Connolly') INFO:sqlalchemy.engine.base.Engine:SELECT USER FROM DUAL ... INFO:sqlalchemy.engine.base.Engine:{'param_1': u'dconnolly'} ('1f8c885f-43e3-4ace-8512-88e65494d59a', <User(dconnolly, Dan Connolly)>)