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:

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.

Outstanding Problems/Defects/Issues

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:

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

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

1. A term hierarchy in CSV format (source:heron_load/curated_data/seer_recode_terms.csv​)
2. 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'

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:

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