Posts for the month of May 2014

HERON Republican: searching by lab value fixed and microbiology positive results available

HERON Republican release allows you to limit laboratory searches to a value for tests with a value assigned. If a lab test does not include a value (e.g., testing positive or negative for influenza) the option to limit by value will not appear. This release also introduces outpatient billing service lines and microbiology positive results.

Remember: any publication that results from a project utilizing HERON should cite grant support (CTSA Award # UL1TR000001).

HERON Republican Contents Summary

This month, our tour of rivers and lakes in Kansas honors the Republican River.

The HERON repository contains approximately 1.5 billion real observations from the hospital, clinics, and research systems:

Observation Patients Source Go-Live Snapshot Issues
Allergy 492K 229K
KUH/O2/Epic Nov 2007 April 2014 various*
Cancer Cases 10.7M 73K
KUH Cancer Registry 1950s April 2014 labels*
Demographics 19.5M 2.04M
KUH Billing (O2 via SMS) 1980s April 2014 various*
UKP Billing 2000 April 2014
27.6K 27.6K Frontiers participant registry Jun 2009 April 2014 #2451
192.8K 192.8K Social Security Death Index 1962 April 2014
Diagnoses (IDC9) 60.7M 750K
KUH/O2/Epic Nov 2007 April 2014 various*
UKP Billing 2000 April 2014
University HealthSystem Consortium (UHC) Q4 2008 Dec 2013
History 25.7M 379K
KUH/O2/Epic Nov 2007 April 2014
Lab Results 139M 346K
KUH/O2/Epic 2003 April 2014 various*
Medications 116M 390K
KUH/O2/Epic (Organized by VA Class) Nov 2007 April 2014 various*
Microbiology 3.05M 27.1K
KUH/O2/Epic 2003 (?) April 2014 various*
737K 115K Negative 2003 April 2014
9.2K 6.97K Positive 2003 April 2014
Nursing Observations 758M ?
KUH/O2/Epic Nov 2007 April 2014 various*
Procedure Orders 154M 527K
KUH/O2/Epic 2003 (?) April 2014 various*
Procedures (CPT) 12.9M 654K
UKP Billing 2000 April 2014 #26
REDCap .96M 45.9K
REDCap July 2011 April 2014
Reports/Notes 58.8M 370K
KUH/O2/Epic ? April 2014
Specimens 110K 8.16K
KUMC Biospecimen Repository ? April 2014
Visit Details 55.8M 813K
KUH/O2/Epic Nov 2007 April 2014
Hospital Quality Metrics 5.91M 80.2K
University HealthSystem Consortium (UHC) Q4 2008 Dec 2013
All 1.4B

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.

Misuse of the Limited Access Death Master File, NTIS, U.S. Department of Commerce data is subject to penalties under provisions of 15 CFR § 1110.200.

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:

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.

#2006
Searching for some lab concepts such as INFLUENZA A NW (#2686) incorrectly prompts the user for numeric constraints
#2413
outdated links from HERON home page
#2595
Micro positive results without sensitivity
#2611
Update HERON system access agreement to include new requirements for SSDMF use
#2655
Load 'Outpatient Billing Service Line Areas' to HERON

Outstanding Problems/Defects/Issues

Learning Object Capability Security with the Online Python Tutor

In Everything Is Broken, Quinn Norton presents an alarming, though witty, case that heartbleed is really just the tip of the iceberg when it comes to computer security problems.

The best weapons I've seen are (a) certified programming with dependent types, and (b) Robust Composition with capabilties.

And on that front, there's great news: sel4, a formally verified, capability based microkernel written in optimized C, is going open source. That's the very lowest layer. At the other end, secure ecmascript lets us use Javascript as an object capability language. Distributed Electronic Rights in JavaScript tells the story at a high level, including which bits are available and which are still in progress. Stuff like the SES node package seems to work pretty well.

Meanwhile, we're a mostly python shop. I've been playing with some python capability idioms for a while. Some of them are a bit obscure, and I've been wondering how to explain our CodeReviewNotes about explicit authority to new developers.

Then I discovered the online python tutor. Perfect!

I hope that trying it out on encap.py will provide enlightenment on the encapsulation aspect of capabilities discussed in From Functions To Objects`. Copy and paste encap.py into the editor and add something like this at the end:

# test
s1 = makeSlot('apple')
print s1.get()
s1.put('orange')
print s1.get()

Then try walking through sealing.py to see how rights amplification works though the motivating example, money.py should be integrated in order for it to really make sense.