Clinical findings

[ShahimEssaid]

Discussion thread for page: https://phenopackets-analysis.readthedocs.io/en/latest/domain-entities/clinical-findings.html

[pnrobinson]

This represents any type of observation of clinically relevant things or situations. 

This is too broad a definition of a clinical finding. Situation can be anything. How about

This represents any type of observation of a clinically relevant abnormality, 
including symptoms reported by patients and recorded in clinical notes, signs 
identified by clinical exam, laboratory test findings, results of imaging or other 
diagnostic studies, results of clinical questionnaires, and other similar findings.

[pnrobinson]

Typo (area):

For our current exome analysis use case we area primarily concerned

[pnrobinson]

Other aspects of the Phenopackets PhenotypicFeature will be addressed based on future driver use cases.

In principle, other important bits of information such as age of onset are available from clinical notes or would be available from data entry software. Even though we may not expect to find say "age of onset" in typical FHIR messages, it seems we could still try to model it, this is quite important for computational differential diagnosis tools.

[pnrobinson]

 However, a PhenotypicFeature will post compose the onset indexed phenotype with Observation components. 

Actually, the APGAR score HPO terms (e.g., https://hpo.jax.org/app/browse/term/HP:0030923) do precompose the onset, but this is a rare exception, the vast majority of HPO terms do not code anything about the onset.

[pnrobinson]

Given that the PhenotypicFeature.severity is a subset of codes for .modifier, 
we can represent this with a single modifier component profile 

I agree, and software can check the actual codes to put them in the right place with the protobuf Phenopacket. Note that the HPO codes are examples and are not required, so it is not true in general that PhenotypicFeature.severity is a subset of codes for .modifier.

[ametke]

All the value set bindings in the current profile are set to required. Based on @pnrobinson comment above I think these should be set to example.

[ametke]

I am wondering if it would be good to have the value of the observation be a concept rather than a boolean, so a value like undetermined can be included. There might be cases where it is relevant to capture the fact that there was an attempt to determine if a patient has a certain phenotypic feature but the results were inconclusive. This is different from the value being true or false and it is also different from not having the phenotypic feature altogether.

[ametke]

I noticed there is a placeholder for the HPO FHIR code system in the core IG that is referenced in the value set bindings of this profile. I have been meaning to work on a proper code system page for HPO and now is probably a good time to do it. The URL that is used here is http://github.com/phenopackets/core-ig/CodeSystem/hpo. The one I have been using is the OWL ontology IRI: http://purl.obolibrary.org/obo/hp.owl. Do you have any preference @pnrobinson ?

[pnrobinson]

Hi @ametke @iimpulse and I were planning on adding this to the HPO build https://github.com/monarch-initiative/phenol/issues/310 -- please join us!

[ametke]

Great, happy to help @pnrobinson !