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https://github.com/orgs/timsbiomed/projects/9/views/1
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HPO: Load to FHIR #33

Open chrisroederucdenver opened 2 years ago

chrisroederucdenver commented 2 years ago

Overview

Pyrophen and a few OWL to FHIR projects exist. We need to see what we need more than just concepts and IDs. Shahim has dealt with (is dealing with) value sets from HPO. Some spelunking to find what can be mined, or what is worth mining from elsewhere, even if just ideas, needs done.

Sub-tasks

Data transformations and content upload for the following FHIR resources that can be created from HPO:

Automation:

Related

joeflack4 commented 2 years ago

@ShahimEssaid I think we've achieved the basic part of this. We've loaded HPO into a server. I guess this is similar to a lot of the other issues where we've essentially got an MVP of it but there's lots of fine tuning we need to do to get this in its optimal state? That's kinda where I am with Mondo on FHIR, for example.

chrisroederucdenver commented 2 years ago

We could stand 2 kinds of additional detail here. What is "basic part"? What more might be desired. It's an analysis task. Having some detail about the first part written down makes the second a little easier. My glance at pyrophen output is that it's basically terms/concepts, no value sets, no maps.

joeflack4 commented 2 years ago

Yeah I'm not sure. You definitely know better than me the extent of our HPO on FHIR work. By basic part, I don't know either. I just know that something HPO related has already been completed. Just don't know what additional updates remain. But this issue would be a good place to enumerate that. I just updated your OP w/ the list of pending updates you mentioned, thanks! (edit: I marked CodeSystem done but I wouldn't be surprised if there are additional tweaks needed on that)

chrisroederucdenver commented 2 years ago

OP?

Let's turn confessions of ignorance into goals to get a more clear picture. @ShahimEssaid has worked with HPO, I think to get some value sets out of it. Others may have more desires.

joeflack4 commented 2 years ago

OP = Original Post That's fine. I added this to the OP:

  1. CodeSystem
  2. ValueSet
  3. ConceptMap

I checked off CodeSystem, but @ShahimEssaid please update the list w/ whatever is done. Maybe none of these are done yet, or are partially done.

chrisroederucdenver commented 2 years ago

I just got off the phone (zoom) with Tim talking about LOINC, comp-loinc and the axioms that Melissa is interested in for LOINC. This came up as a more accessible way to finally learn more OWL etc. I guess HPO, being an ontology is more consistent than LOINC and is more beginner friendly. I will make time and fire up Protege and have a look around. I can loop you in as I make sense of it. Lemme know your interest and time etc. No worries if busy.

joeflack4 commented 2 years ago

Oh, I see. This is related to your comment (and my response) in the other HPO issue: https://github.com/HOT-Ecosystem/hapi-fhir-jpaserver-starter/issues/1#issuecomment-1262898963

I'm a little involved with CompLOINC so I have a decent grasp of what Tim's doing. I am having a really packed week though, and I think the next week or few are going to be the same, so I probably won't have time to chat about it outside of the TIMS dev meeting.