NHANES data in LibreEHR

Ok. Will generate and send ssh key

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There are some new minor edits to the Mission and Vision statement so would appreciate input. I have heard nothing about creating a new web page so we can start posting content under the Educational EHR initiative.

I decided to post the Mission/Vision statement on Google Drive so it could be easily accessed and modified. I threw in a curve ball, asking if we should consider a commercial partner to help fund our efforts for future modifications, as opposed to solely depending on NIH/NSF type grants. Just trying to solicit as many opinions as possible.

I tossed Java 8 onto the EHR server(which hosts both the EHR Demo and the NHANES demo)

Weka is primarily used using a GUI. So, I dont think installing Java 8 on the server will be useful. Weka is run on the client side for doing data mining, unless one writes a wrapper or uses the CLI tools of Weka

it’s installed anyways…and I’m not opening the database to the outside world…so CLI may be necessary

I did post a short blurb on our LibreHealth Educational EHR initiative on my blog today. Just gave general information. Easy to change if anyone sees an error

LibreHealth EHR is part of a 2016 initiative by the developers of OpenMRS and OpenEMR.

Please say former – this implies that OpenMRS and OpenEMR endorse the work – they don’t. OpenEMR especially does not. The project is run by FORMER developers of OpenMRS and OpenEMR.

Changed to former. Thanks for the input

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The PowerPoints on educational EHRs have been created for the Inspire presentation on June 7th. Hopefully, the lab data will be uploaded by then. Ideally, we should have a landing web page on the educational LibreHealth EHR as well

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With help from Sunbiz, we now have a landing page for the educational EHR project. LibreHealth.io >> Teams >> Education and university outreach. There are a few issues, but a good start.

Thanks to Kevin Yeh we have CSV files on all of the exams for the NHANES 2011-2012 era. We have only uploaded a small number of these files but just having them available in an easy to analyze format is a huge plus. I opened the 126 folders and gave them all common sense names ( NHANES Tables and Files.pdf (29.4 KB)

Each folder has multiple tables within it. I think when we are ready to launch and publicize the project we should make these CSV files available, along with the SQL dump file. Thanks to everyone for their hard work

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We should discuss whether we would like to create a core set of sample patients, using the NHANES data, that depicts average US patients and common diagnoses. It would not be hard to add some more demographics and insurance information, an encounter and perhaps an image/report.

I did see where you could upload an image (JPEG) in the patient summary >> documents >> lab reports. So Jimmy Jennings now has a chest xray showing COPD, which is one of his problems and a carotid US. Is that were images and/or image reports should go?

I just updated the dataset on the server. Lab Values are there now as “procedures orders/results.” One needs to look at the created encounter for each patient to view the data.

I’m treating all the data as a single “NHANES Lab Panel” rather than as their component parts. (BMP,CBC,A1c,TSH etc…) as it made the import process much simpler.

Updated version of the SQL download is available here: https://nhanes.librehealth.io/download/withLabData.sql.gz

This covers all the major pieces of data to be imported at this point. There are a few small details missing that I will circle back to, (race, income for example…) However, I’m going to generate queries for the CQM analyses for Blood Pressure and A1c I mentioned in the initial proposal first.

Dr. Hoyt, to update the system, I replace the existing database. I tried to preserve the images you added, which I think I did successfully, but sorry if I destroyed any content I wasn’t aware of.

Thanks, that’s wonderful news. I’ll be playing with the lab data this weekend. No problem if images were deleted. Hope everyone has a great and safe Holiday weekend

I now see results for Jimmy Jennings but the range is empty. Is there a “list” where I can input the normal range for e.g. HDL cholesterol?

If we have a list of normal ranges for each of the tests, I can add them to the import process. I can also flag the results as “normal or abnormal” in the system.

  1. Looks like the path is to identify a patient, then go to Lab Overview and check the boxes for the tests which are categorized by LOINC numbers. Is there an easier way??
  2. No two patients have the same number of tests, which is fine
  3. Most chemistry result ranges can be found on e-medicine
  4. For hemoglobin A1C if it is 6.5% or higher it is abnormal and diagnostic of diabetes
  5. For the spot urine albumin/creatinine ratio what is recommended is as follows: Normal Ratio (in general <30 mg/g is normal) Men: < 0.017 (or 17 mg albumin to 1 gram Creatinine) Women: <0.025 (or 25 mg albumin to 1 gram Creatinine) Microalbuminuria: 30-300 mg albumin/g Creatinine Macroalbuminuria: >300 mg albumin/g Creatinine
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Did we share the EHR now with potential educators or you are planning to do so at Inspire … would be great to have some early feedback on what folks think

The time allotted to discuss offline educational EHRs on the InSpire panel is very short and is a topic that the panel moderator is not interested in. He wants to modify production EHRs, like Epic to have an educational component. That is what he wants the panel to present/discuss. Probably the best that I can do is link the few PowerPoint slides I will present to our web site and comment that I would be happy to talk to people offline about it.

Because I am on the AMIA educational working group, I could probably present this project to them, but it is only a small group.

I now have a listserv of 452 health informatics instructors who have requested a download of my textbook, so I have used/abused this group for input on several subjects. I think the LibreHealth education team must first discuss our approach going forward and then reach out to educators. We have not really had a meeting yet to brainstorm

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Also, the fastest way to see lab work on our patients is on their Summary Sheet >> Trends Lab

Pam Charney from Bellevue College has requested more information about the project. I will speak to her in person at the InSpire conference and gave her the demo information. This is significant because she is looking for a better student-EHR experience and Bellevue seems to get a lot of HIT training dollars from the feds

To the Education Team: Should we create a new Forum post category “Education Team” so we can discuss the way forward?

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