Bell Eapen

Physician | HealthIT Developer | Digital Health Consultant

Rendering FHIR Questionnaire for data capture

Standardized data collection forms are vital for health information systems. This is particularly true in public health, where there is a host of data collection forms shared by various organizations. InterRAI is a typical example. Standardization is important for collaborative data analytics at various levels, a need that became painfully apparent during the recent COVID-19 pandemic.

Google  Nevit Dilmen  Slawek Borewicz  Commons-emblem-question blue / CC BY-SA (https://creativecommons.org/licenses/by-sa/3.0)
Google Nevit Dilmen Slawek Borewicz Commons-emblem-question blue / CC BY-SA (https://creativecommons.org/licenses/by-sa/3.0)

Though standardization of content is widely addressed, the standardization of the form appearance and rendering is less so. Many healthcare teams find their information systems incapable of dealing with this requirement. They have to often resort to expensive resources to create these forms using various technologies such as javascript. It is not easy to share such electronic forms (E-Forms) with other organizations because of the different requirements of the host systems.

The HL7 FHIR Questionnaire is emerging as a standard that is capable of dealing with both the content and presentation of E-forms. We proposed the FHIRForm framework to use this standard for form management and introduced an open-source stack for form management. One of the components of the framework is an npm module (javascript) to convert the FHIR Questionnaire resource to a JSON schema that can be used by popular form rendering libraries can use. The component called FHIRFormJS can also convert the form submission into a QuestionnaireResponse resource that can be submitted to any FHIR compliant servers.

FHIRFormJS was a work in progress for a long time and was not really stable enough to use. I am excited to introduce the new version of FHIRFormJS that is better and easier made possible by the @ahryman40k/ts-fhir-types library. If you have been using older systems such as LHC-Forms, give FHIRFormJS a try and let me know how we can improve it. Pull requests are most welcome and I have added this repository as a hacktoberfest participant. There is also a sample react application that uses FHIRFormJS (repository link above). If you are using Vue, I have a separate library that targets one of the popular form rendering engines for Vue.

Let me know if you find this interesting and use the GitHub issues for feature requests.

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Counting conditional Occurrences using Prolog.


Counting conditional occurrences using Prolog.

I wanted to implement the following rule in prolog for my IISA project.

If the percentage of coil region is greater than 20% the homologue detection algorithms may become unreliable. The coil module of IISA returns prolog database in the following format.

coil(105,a,0.000).
coil(109,g,0.001).
coil(110,l,0.004).
coil(111,l,0.014).
coil(112,v,0.055).
coil(113,g,0.055).
coil(114,s,0.371).
coil(115,e,0.416).
coil(116,k,0.860).
coil(117,v,0.955).
coil(118,t,0.998).
coil(119,m,0.999).
coil(120,q,0.999).
coil(121,n,0.999).

ie coil(position, aminoacid, probability of being part of coil).

I wanted to count the number of facts with the probability exceeding a cutoff value, say 0.7.

Though it is simple problem, I could not find any solution for this even after googling for few hours. Finally I found this code on the net.

%Code to count the number of proofs for a goal. Found on the net.
count_proof(Goal, N) :-
            flag(counter, Outer, 0),
            (   call(Goal),
                flag(counter, Inner, Inner+1),
                fail;
                flag(counter, Count, Outer),
                N = Count
            ).
Though it worked well (I have still not figured out how!) the code is SWI-Prolog specific and did not work in JLog prolog applet I use for IISA web interface.

Finally I learned about findall and bagof
But still it took some time to figure out how to use findall for my purpose because the description read findall (Var, Database, Array) and to use length(Array). Using coil (_,_,A) as database will count only the number of aminoacids and I didn’t know how to implement the condition A>0.7.
Finally somewhere I found the actual definition for findall (Var, Goal, Array) which solved my problem, though I wasted a whole day on this simple problem.

Here is the final code.

%The region is coil if the value is greater than threshold
coil_region(Cutoff, Val):-
                     coil(_,_,Val),
                     Val>Cutoff.
                    
coil_percent(Region, Total, Percent):-
                     setting(coil,X),
                     findall(Val,coil_region(X,Val),R),
                     length(R,Region),
                     findall(C,coil(_,_,C),A),
                     length(A,Total),
                     Total>0,        %Avoid division by zero
                     Percent is (Region/Total) * 100,!.

coil_percent(0,0,0).

IISA Home Page.

Zostavax

Merck recently gained approval for a vaccine called Zostavax for preventing herpes zoster reactivation in elderly people. This live virus vaccine is unusual in that it is to prevent reemergence, not to prevent initial infection. Can the same concept be used for recurrent herpes simplex infection which is much more disabling than herpes zoster in younger people?

Vigyaan CD Part II [NX SERVER]

Running NX server & accessing it from windows machines.

To start NX server, click on KNOPPIX -> Services ->NX server.

The script is supposed to add a new user called nxuser. However this functionality is not working properly in Vigyaan 1.0. Hence you have to use the root account or the default knoppix account. But by default both these accounts do not have passwords. Hence you have to set a password for both these accounts.

Click on the terminal icon on status bar.
su
passwd
<change the password>
Close the terminal window
System ->kduser
Select knoppix
Uncheck Disable account’
Click Set password and set a new password.

Now on your windows machine download and install nx client from NOMACHINE.

Find the local IP of the vigyaan box by typing ifconfig in a terminal window. Now you can access vigyaan box from your windows machine.

Coiled Coils

Coiled coils consist of two to five amphipathic alpha-helices that twist around one another to form a supercoil which can be left-handed or right-handed. Left handed ones show a seven-residue periodicity and the right handed one a 11 residue periodicity the stability of which is achieved by a knobs-into-holes packing of apolar side chains into a hydrophobic core.


By modulation of their polar interactions, many different properties like extreme thermo stability can be achieved. Coiled coils are involved in signal transduction or molecular recognition. They provide mechanical stability to cells and are involved in movement process. Charged residues are frequently found at coiled coil interfaces.

The building blocks of IF architecture is an elongated coiled coil region (which inturn contains monomeric 1A and dimeric 1B, 2A and 2B sub segments connected by short linkers) flanked by non helical end domains. The dimeric 2B contains a discontinuity in the heptad repeat pattern called a stutter that creates an undecad repeat which is important for its structural integrity. The highly conserved region within the C-terminus of 2B has an inter-helical and intra-helical salt bridge.

There are several software products to predict the coiled coil region of proteins based on the above structural peculiarities.

References:
Peter Burkhard et al. Coiled Coil: a highly versatile protein folding motif. Trends in Cell Biology 2001:11(2); 82-8


VigyaanCD





Setting Up your own Bioinformatics workstation using VigyaanCD

VigyaanCD at
http://www.vigyaancd.org/
has a nice collection of bioinformatics software and is worth downloading. It will boot directly from the CD and needs very little linux expertise as the X-windows system is almost like windows. However I wanted to use it along with windows and I did not want to reboot every time I switch operating system. This is the story of how I set up VigyaanCD on a second hand PIII and use it from my win XP laptop.

I bought a second hand IBM PIII, 450 MHz, 10MB HDD and 128 MB RAM. I formatted the hard disk and added the following partitions
/boot 2GB (ext2), /knophome 6GB (ext2) /knopswap (vfat) /dos (vfat)
My video card supports only 800×600

I copied the CD image to the boot partition with the knoppix tohd =/dev/hda1 command. I created a persistent home directory in /knophome partition and a swap in /knopswap

I start with the following command.
Knoppix screen=800×600 fromhd home=scan noprompt noeject

I will write about how to set up the NX server and run the NX client from laptop to access it in my next post.

PLoS Clinical Trials


Clinical trials, particularly randomized trials are critical in delivering reliable evidence about the efficacy of an intervention. Clinical trial data can also provide important information about the potential adverse effects of treatment. Currently, not all trials on human participants are reported in the peer-reviewed literature. PLoS Clinical Trials aims to fill this gap. As an open-access journal, all articles published in the journal will be immediately and freely available online. Join them in supporting these goals, and get your paper read by the widest possible audience: submit your trial results today.
[Download Poster.]

Good Clinical Practice GCP

Good Clinical Practice (GCP) guidelines

GCP has two important goals: protection of the subject, and protection of the data which is possible only through adequate training of all concerned staff. An independent audit is needed to ensure compliance to the standards. US FDA acts as enforcement officers. As they are less flexible unconventional approaches have no scope. European agencies are more flexible but they need to be convinced.

The Declaration of Helsinki issued by world medical association insists that all research subjects must be fully informed about the nature and risks of a clinical trial. Protocol design is a responsibility of the investigator and need to be assessed by the concerned ethical committee. The principal investigator has an overall responsibility over the entire project.

Informed consent which includes signing a consent form and a recruiting interview preferably by the physician is extremely important. Though not absolutely necessary it is a good practice to define and describe in writing how all aspects of clinical research are to be conducted. These standard operating procedures (SOPs) must be followed during the execution of the research.

Translation


Translation

Today I learnt few concepts in protein expression which I found very interesting. As we all know, because of the redundancy of the triplet code, it is possible to preserve aminoacid sequence coding while varying the nucleic acid code. This can even happen as a silent mutation. However the availability of corresponding tRNA for each triplet varies from species to species. The translational efficiency of each code may be different (some times to a very great extend) though all may code for the same product. All silent mutations may not be silent after all.

Few codon pairs exist in relative abundance which may act as translation pause sites and slow down translational process. The tRNAs that bind during the translation of such a biased pair appear somehow incompatible. These codon pairs vary from species to species.

These points need to be considered while designing a gene for expression systems. Designing and implementing an algorithm to optimize the gene with respect to the above points can be a good bioinformatics project.