Add link to LOINC2HPO

[pnrobinson]

I am ready to go but could somebody please answer the following questions

• [ ] Does it make sense and is it possible to add a version of HPO on FHIR? Does cd2h include a FHIR-server?
• [ ] What is the intended audience? I would like to optimize the demo use case for the command-line code we have.

[mellybelly]

@pnrobinson @kingmanzhang any update? I know there were other tickets/discussions, please let @eichmann know how to best help get a demo up on Labs.

Audience is the CTSA community, largely informatics people. They will be interested in your asthma use case, but also rare disease or data quality examples.

[kingmanzhang]

I am unclear what is expected here. @mellybelly Do you mean adding a link to the project on the Labs page? (http://labs.cd2h.org/labs/) We already have a link to ehr2hpo on the CD2H Project Dashboard.

[mellybelly]

@kingmanzhang the requirement is working code online - it can be a demo with fake data.

[kingmanzhang]

Our high quality code is the fhir2hpo library and the smart on fhir app. The smart on fhir app can be demonstrated with a Smart sandbox, which I assume Amy has implemented. @aeyates An alternative is the loinc2hpo codes, which also has a user interface that allows one to simulate data and convert to HPO. @pnrobinson I have the asthma analysis code as a command line (https://github.com/TheJacksonLaboratory/HUSHDataAnalysis/blob/7c77e2eed13bed457beafafb32004f9f672cef96/src/main/java/org/jax/App.java#L879), although I would feel embarrassed to use it as a demo case. It is really dirty code to get the job done without thinking about reusing it.

I recommend the first two options. I am with Amy at the AMIA conference. We can make sure that one or both options work correctly for the task force meeting tomorrow. If you want to choose the third option, I will have to spend some time to clean it up, which is hard to finish before tomorrow.

[aeyates]

@pnrobinson @mellybelly @kingmanzhang @eichmann We could host a public link to the HPO on FHIR application against one of the FHIR sandboxes. Would that be useful? Can we host this through our regular workflow at octri.ohsu.edu, or do you need this on some server at NCATS? It would be fairly easy for us to provide a docker container if that's the better way to go for visibility.

[mellybelly]

Thanks @kingmanzhang ! I think either or even both of the first two options would be terrific. Remember the goal is to get early feedback on products in development. The most important thing is to let people know what is happening.

@aeyates yes that is exactly what i am thinking. it doesn't matter where it is located, @eichmann can wrapper no matter where it lives. Docker would be great too.

[aeyates]

Great, I saw @eichmann in a previous session. I'll look to connect in person today.

[kingmanzhang]

Great. I think we agreed on letting Amy adding a link to the SMART on FHIR app. @aeyates I can show you how to run my GUI really quickly just in case it is needed.

[pnrobinson]

@aeyates -- I have heard that Docker has some security issues and that Singularity is a better option -- we are probably going to be using Singularity for another project here. If you agree, let's go for Singularity instead of Docker. (https://singularity.lbl.gov/)

[aeyates]

@pnrobinson Our team is currently very tied to Docker and it's quickly becoming the defacto standard for quick containerization throughout the software development world. If you can point us to documentation about security issues, I can review it with my team. But for the proof of concept, we are not exposing any real data, nor is the app even backed by a database. We were able to stand up an instance quickly despite everyone being on vacation. It's hosted here: https://octri.ohsu.edu/hpo_on_fhir/ @mellybelly @kingmanzhang @eichmann

[eichmann]

@aeyates Then I'm good to add a link on labs to this url?

[aeyates]

Yes please. Thanks @eichmann !

[eichmann]

Done.