Applied Bimatics - An Informatics & eHealth Blog

I am a clinician with a passion for informatics. This blog is about my eHealth journey exploring interoperability in Electronic Medical Records (EMR/EHR), Patient Safety, Pharmacovigilance, Data Analytics, Clinical Research and Bioinformatics in a clinical context. Comparing Canadian, Indian and Middle Eastern healthcare systems and services. Join our open facebook group here: https://www.facebook.com/groups/clinical.bioinformaticians/


GIT for doctors (Part 3) - stash, branch, merge, rebase and tag

To continue with our git story: (Read the full series on GIT for doctors and healthcare professionals here.)

If you think you have made a mistake, you can “stash” the changes. Your file will be returned to the previous state. You have the option of returning to the stash if needed, but this is beyond our scope at present.


Now let us consider another scenario: You have two differential diagnosis for your patient and you want to investigate the patient for both conditions. You may decide to keep two versions of the same case sheet to continue the work up on both differentials. In Git you can create a “branch” for this situation. You can work on branches independently. The main branch or the trunk is called “master” by convention. You can give any name for the other branches.

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Psoriasis support : eHealth gaming tools for patient engagement

Psoriasis manum
Psoriasis manum (Photo credit: Wikipedia)

Here is the IFPA  survey to compare 17 different strategies and activities that can be used to advance psoriasis education, advocacy and awareness. Preliminary results of the survey will be presented on World Psoriasis Day and the final results will be announced at the 4th World Psoriasis & Psoriatic Arthritis Conference in Stockholm July 8-11, 2015.

I have listed below some of my random ideas on eHealth tools for patient engagement in psoriasis:


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Resource Description Framework (RDF) and Population Informatics

English: A PICTURE OF A RDF
A PICTURE OF A RDF (Photo credit: Wikipedia)
I have been an RDF fan even before I used it for dermbase. I promptly signed the Yosmite Manifesto and blogged about it last year. After gaining more experience in the regional health information exchange initiative(s), I still feel that RDF is important, but in a different way.

Most federated regional clinical viewers query host databases, convert the results into an intermediary format (mostly xml or HL7), apply filters and then provide a consolidated view in the browser and mobile as html embellished with jQuery. Though this seems not-so-scalable technology, it works remarkably well in a regional context. Federated clinical viewers also attempt to create data warehouses on top of the Clinical Viewer. Such data warehouses have enormous potential in population informatics and RDF could be an ideal framework for this purpose.

RDF is a proven technology that is schema agnostic. However in this context the biggest advantage of RDF is its data-atomic nature that enables each data element to be queried, changed, or deleted independent of any other data element. RDF blank nodes can be used to effectively anonymize the data. From a data analytics perspective representation in the RDF format makes data amenable for “reasoning” to discover new knowledge.

Genomic data analytics has revolutionized pre-clinical research. Growing popularity of Health Information Technology (HIT) and Health Information Exchange (HIE) has not yet resulted in a similar impact on population health. There are some fundamental differences between genomic and clinical data.

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SUSie: SUS based questionnaire for assessing usability and physician attitude toward health information exchange

evaluation of eyetracking after an usability test
evaluation of eyetracking after an usability test (Photo credit: Wikipedia)
Health information exchange (HIE) allows healthcare providers and patients to access and securely share medical information electronically. Several organizations are now emerging to provide both form and function for HIE efforts, both on independent and governmental/regional levels. However the biggest challenge is Change Management, as healthcare providers are exposed to one more ICT tool that they need to master for providing quality care.

There are no formal tools to study individual and organizational attitude towards HIE or to measure their usability. Physician attitude towards the impact of HIE on reducing healthcare costs, improving quality of patient care, saving time and their concern about data privacy and security are important in HIE adoption. Usability is also of vital importance in the meaningful use of HIE tools.

SUSie (SUS for HIE) is an attempt at creating a useful tool for measuring the above factors. It is modelled based on System Usability Scale (SUS), one of the most used questionnaire for measuring perceptions of usability. Five additional questions were added to assess factors that are specific for HIE. The scoring is based on a scale of 5 ranging from Strongly disagree(1) to Strongly agree (5). The ratio of positively and negatively worded questions are maintained and the final multiplication factor was changed to 1.67 to represent the final score on a scale of 100. I hope that this would make the interpretation similar to SUS and benefit from the prior experience available for SUS. The questions and details of scoring are explained below.

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Git for Doctors and healthcare professionals - 2

Read Part 1

Imagine that you have a patient's case file in a folder on your computer. The file has many contents such as history sheets, lab reports and discharge summaries.

[Create a folder in your computer with few word files. This folder is your case file.]

Since the case file is precious, you want to take a photocopy before you change/add anything to the file. So you decide to buy a photocopy machine. In 'GIT' instead of the photocopy machine you 'create a repository'

[Click on create repository and choose the folder.]

Now you have to decide what to photocopy. Let us say, you decide to photocopy everything. Deciding what to photocopy is called staging in GIT.

[Select All – and 'Add to Index']

Now go ahead and take the photocopy. In GIT it is called Commit

[Click commit]

Congrats.. You have photocopied the contents. Now you can safely add your comments.

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GIT for Doctors & healthcare professionals - I


Type 36 JSDF Arm Suit
Type 36 JSDF Arm Suit (Photo credit: Mechanekton)
GIT for us doctors is an acronym for GastroIntestinal Tract. But the GIT I am going to talk about here has nothing to do with GastroIntestinal tract. Do you have any gut feeling about what it is going to be?

Well, GIT according to wikipedia is a distributed revision control and source code management (SCM) system with an emphasis on speed. What has that got to do with healthcare professionals and doctors? As healthcare is becoming tech savvy, healthcare professionals and some doctors have started to recognize and understand, not just completed software products, but their source code as well.

The rising prominence of open-source movement in healthcare will greatly benefit from this, as doctors start contributing actively to healthcare application design and code. When you contribute code to an open-source project, there should be a mechanism to download what others have done, maintain concurrency as others keep adding things, keep track of what you add along with others who contribute, and finally impress the master with your contribution. This process is much more complex than the conventional version control or keeping track of older version by keeping copies of different stages. So that is where GIT steps in.

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Electronic Health Records heartbleed

Open Source Media Framework Icon
Open Source Media Framework Icon (Photo credit: Wikipedia)
Finally we presented our ultra small EHR project (TED) on wednesday with the promise of pushing it into GitHub as an open-source project soon. The biggest challenge in small turnkey EHRs is data security and privacy. While we were presenting our project the world was desperately seeking the patch for the Heartbleed bug and CRA Canada shut down its portal to avoid any potential data security breach. We are still not sure about the impact of this bug worldwide. So what exactly is heartbleed and how can it effect the burgeoning open-source revolution in health informatics?

Heartbleed is a bug in a widely used open-source encryption method called openSSL. When two computers are securely connected by this method there is a mechanism for periodic checking of this secure connection. We now know that this process was not secure after all, as there was a flow in this method that made the data in the RAM of the computers potentially visible to intruders. The data in the RAM of the computer at any time is likely to be the most sensitive including information such as passwords. This vulnerability was present for almost 2 years till it was spotted recently. Though the obvious question at this point is, who knew about this vulnerability before, the potential ramifications of heartbleed extends right to the heart of the open-source philosophy in secure software systems such as EHRs.

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About Me

As a Dermatologist and Informatician my research mainly involves application of bioinformatics techniques and tools in dermatological conditions. However my research interests are varied and I have publications in areas ranging from artificial intelligence, sequence analysis, systems biology, ontology development, microarray analysis, immunology, computational biology and clinical dermatology. I am also interested in eHealth, Health Informatics and Health Policy.

Address

Bell Raj Eapen
Hamilton, ON
Canada