HERON Cow Creek release includes order sets and analysis tool enhancements
Previously, the Multi-Cohort Survival Analysis tool had the option to limit by 5 years, 10 years or All. This release expands that option to weeks, days, or hours in addition to years. The Timeline analysis tool increases granularity to display by the hour as opposed to day as in previous releases.
The Cow Creek release introduces order sets as a new searchable data type. This release also kicks off the ability to limit MAR by dose.
HERON Cow Creek Contents Summary
This month, our tour of rivers and lakes in Kansas honors Cow Creek.
The HERON repository contains approximately 1 billion real observations from the hospital, clinics, and research systems:
Observation | Patients | Source | Go-Live | Snapshot | Issues | |
---|---|---|---|---|---|---|
Demographics | 18.6M | 1.96M | ||||
KUH Billing (O2 via SMS) | 1980s | Feb 2013 | various* | |||
UKP Billing | 2000 | Feb 2013 | ||||
15.8K | 15.8K | Frontiers participant registry | Jun 2009 | Feb 2013 | ||
187.8K | 187.8K | Social Security Death Index | 1962 | Feb 2013 | ||
Diagnoses (IDC9) | 44.1M | 667K | ||||
KUH/O2/Epic | Nov 2007 | Feb 2013 | various* | |||
UKP Billing | 2000 | Feb 2013 | ||||
University HealthSystem Consortium (UHC) | Q4 2008 | Dec 2012 | ||||
History | 15M | 302K | ||||
KUH/O2/Epic | Nov 2007 | Feb 2013 | ||||
Medications | 91M | 313K | ||||
KUH/O2/Epic (Organized by VA Class) | Nov 2007 | Feb 2013 | various* | |||
Nursing Observations | 585M | ? | ||||
KUH/O2/Epic | Nov 2007 | Feb 2013 | various* | |||
Lab Results | 85.2M | 295K | ||||
KUH/O2/Epic | 2003 | Feb 2013 | various* | |||
Order Sets | 275K | |||||
KUH/O2/Epic | 2003 (?) | Feb 2013 | various* | |||
Procedure Orders | 117M | 450K | ||||
KUH/O2/Epic | 2003 (?) | Feb 2013 | various* | |||
Procedures (CPT) | 10.8M | 585K | ||||
UKP Billing | 2000 | Feb 2013 | ||||
Reports/Notes | 38M | 288K | ||||
KUH/O2/Epic | ? | Feb 2013 | ||||
Specimens | 47.4K | 4K | ||||
KUMC Biospecimen Repository | ? | Feb 2013 | ||||
Visit Details | 28.5M | 539K | ||||
KUH/O2/Epic | Nov 2007 | Feb 2013 | ||||
Cancer Cases | 9.8M | 67.1K | ||||
KUH Cancer Registry | 1950s | Feb 2013 | labels* | |||
Hospital Quality Metrics | 5.10M | 69.2K | ||||
University HealthSystem Consortium (UHC) | Q4 2008 | Dec 2012 | ||||
Triple Negative Breast Cancer Registry (BRCA) | 27.6K | 161 | ||||
REDCap | July 2011 | Jan 2013 | #1741 | |||
All | 1.09B |
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
Due to in-progress trac access policy issues, this section may be blank for a time.
- #1526
- Load Orderset Usage into HERON
- #1685
- Add sponsor, title, and description to HERON Usage Audit Report
- #1742
- multi-cohort survival plugin fails to initialize after the 1st time
- #1835
- HERON uses ICD-O-2 labels for ICD-O-3 morphology/histology cancer tumor registry codes
- #1849
- flexible time windows for HERON Multi-cohort survival analysis tool
- #1891
- handle times, not just dates, in i2b2 timeline in HERON
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 |
HERON Bow Creek Release brings Cancer Survival Analysis, R integration
The highlights for this release include:
- interactive cancer survival analysis plotting plug-in, building on our initial tumor registry integration.
- "same visit" queries (#790), building on our initial i2b2 1.6 upgrade
Our cancer survival analysis plug-in is based on work by Segagni et. al.:
- J Am Med Inform Assoc. 2011 May 1;18(3):314-7. Epub 2011 Jan 24. R engine cell: integrating R into the i2b2 software infrastructure. Segagni D, Ferrazzi F, Larizza C, Tibollo V, Napolitano C, Priori SG, Bellazzi R.
- i2b2-r-engine-project on google code
- R Engine Cell in Orbit
HERON Bow Creek Contents Summary
This month, our tour of rivers and lakes in Kansas honors Bow Creek river.
The HERON repository contains approximately 600 million real observations from the hospital, clinics, and research systems:
Observation | Patients | Source | Go-Live | Snapshot | Issues | |
---|---|---|---|---|---|---|
Demographics | 16.0M | 1.89M | ||||
KUH Billing (O2 via SMS) | 1980s | Dec 2011 | various* | |||
UKP Billing | 2000 | Dec 2011 | ||||
8.18K | 8.18K | Frontiers participant registry | Jun 2009 | Dec 2011 | ||
182K | 182k | Social Security Death Index | 1962 | Dec 2011 | ||
Diagnoses (IDC9) | 17.9M | 586K | ||||
KUH/O2/Epic | Nov 2007 | Dec 2011 | various* | |||
UKP Billing | 2000 | Dec 2011 | ||||
Medications | 28.0M | 103K | ||||
KUH/O2/Epic | Nov 2007 | Dec 2011 | various* | |||
Nursing Observations | 434M | ? | ||||
KUH/O2/Epic | Nov 2007 | Dec 2011 | various* | |||
Lab Results | 69.8M | 248K | ||||
KUH/O2/Epic | 2003 | Dec 2011 | various* | |||
Procedures (CPT) | 9.4M | 531K | ||||
UKP Billing | 2000 | Dec 2011 | ||||
Specimens | 25.5K | 2.66K | ||||
KUMC Biospecimen Repository | ? | Dec 2011 | ||||
Cancer Cases | 8.96M | 61.9K | ||||
KUH Cancer Registry | 1950s | Dec 2011 | labels* | |||
All | 606M |
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
No results
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 |
Adding SEER Site Recode to HERON Tumor Registry integration
Our HERON tuttlecreek release a couple months ago included initial integration of data on ~60,000 cancer cases from the KUMC tumor registry. We organized the NAACCR terms based on work by colleagues at the Kimmel Cancer Center in Philadelphia and Group Health Cooperative in Seattle:
But if you want to find, for example, brain cancer cases, due to an outstanding issue (#733), you have to be an expert in codes for primary site, histology, etc.:
For our next release, based on work with John Keighley, we're providing query by SEER Site Recode, a state of the art method for combining primary site and histology:
Under the hood: Using python to convert the rules table to SQL
The SEER Site Recode ICD-O-3 (1/27/2003) Definition, lays out the rules in a fairly convenient HTML table:
Converting that table to code manually might have been straightforward, but it would have been repetitive and error-prone; so like so many Geeks and repetitive tasks, I wrote a script to automate it.
source:tumor_reg/seer_recode.py weighs in at about 200 lines, including whitespace and a handful of test cases. It reads the HTML page (well, I feed it through tidy first to clean up some table markup) and produces
- A term hierarchy in CSV format (source:heron_load/curated_data/seer_recode_terms.csv)
- Rules to recode our our ~60K cancer cases as a SQL case statement (source:heron_load/seer_recode.sql).
The resulting SQL weighs in at about 500 lines. Handling all the different kinds of rules in the table was fun; a lot more fun than writing this sort of SQL by hand:
case /* Lip */ when (site between 'C000' and 'C009') and not (histology between '9590' and '9989' or histology between '9050' and '9055' or histology = '9140') then '20010' ... /* Melanoma of the Skin */ when (site between 'C440' and 'C449') and (histology between '8720' and '8790') then '25010' ... /* Cranial Nerves Other Nervous System */ when (site between 'C710' and 'C719') and (histology between '9530' and '9539') then '31040' /* ... */ when (site between 'C700' and 'C709' or site between 'C720' and 'C729') and not (histology between '9590' and '9989' or histology between '9050' and '9055' or histology = '9140') then '31040'
HERON Tuttlecreek release brings initial Tumor Registry integration
This month's HERON release integrates data from the KUH Tumor Registry, with 65,000 cases dating back to the 1950s(#547). We have also added support for finding patients in KCK county school districts (#531).
Russ regularly gives presentations on our work, describing the integration of various sources into HERON. Since this diagram from How Medical Informatics and HERON Can Help Your Research?, given on November 17, we have integrated the Social Security death master file as well as the tumor registry:
HERON Tuttlecreek Contents Summary
This month, our tour of rivers and lakes in Kansas honors Tuttle Creek Lake.
The HERON repository contains approximately 570 million real observations from the hospital, clinics, and research systems:
Observation | Patients | Source | Go-Live | Snapshot | Issues | |
---|---|---|---|---|---|---|
Demographics | 15.9M | 1.88M | ||||
KUH Billing (O2 via SMS) | 1980s | Oct 2011 | various* | |||
UKP Billing | 2000 | Oct 2011 | ||||
6.64K | 6.64K | Frontiers participant registry | Jun 2009 | Oct 2011 | ||
Diagnoses (IDC9) | 17.2M | 571K | ||||
KUH/O2/Epic | Nov 2007 | Oct 2011 | various* | |||
UKP Billing | 2000 | Oct 2011 | ||||
Medications | 26.3M | 96K | ||||
KUH/O2/Epic | Nov 2007 | Oct 2011 | various* | |||
Nursing Observations | 407M | ? | ||||
KUH/O2/Epic | Nov 2007 | Oct 2011 | various* | |||
Lab Results | 67.2M | 240K | ||||
KUH/O2/Epic | Nov 2007 | Oct 2011 | various* | |||
Procedures (CPT) | 9.1M | 523K | ||||
UKP Billing | 2000 | Oct 2011 | ||||
Specimines | 23.1K | 2.48K | ||||
KUMC Biospecimine Repository | ? | Oct 2011 | ||||
Cancer Cases | 6.21M | 60.4K | ||||
KUH Cancer Registry | 1950s | Aug 2011 | labels* | |||
All | 570M |
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)
Problems/Defects/Issues Addressed in this Release
No major issues addressed.
Outstanding Problems/Defects/Issues
No results