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biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology
https://biolink.github.io/biolink-model/
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Exposure outcome modeling #461

Open karafecho opened 3 years ago

karafecho commented 3 years ago

A clear and concise description of what the request is.

I want to represent exposure outcomes in Biolink.

What working group (or team) did this request originate from?

The need for representing this type of data originated from the Translator 2020 exposure-outcome breakout session on 9/23/2020..

Note:

This is relevant for members of NCATS Translator.

Describe the solution you'd like

We'd like to define new outcome semantic types (other than phenotype or disease) and identify a general approach for representing outcome metadata.

Additional information to support this request

image

**Tag relevant members for discussion

@karafecho @diatomsRcool @stevencox @xuhao

deepakunni3 commented 3 years ago

Would biolink:DiseaseOrPhenotypicFeature work for representing outcomes? Or is that too misleading in terms of representation?

Another way would be to have biolink:Outcome as a sibling to biolink:DiseaseOrPhenotypicFeature

karafecho commented 3 years ago

The challenge is that outcomes such as 'ED visits' or 'hospital readmission' or 'surgical intervention' do not really map to DiseaseOrPhenotypicFeature. 'Sibling' might work, but I'm wondering if outcomes are better modeled as 'outcome events', akin to 'exposure events'? I'm by no means an expert, however, so my suggestions may not make sense.

Thanks for looking into this!

karafecho commented 3 years ago

During Friday's meeting of the Clinical Data WG, I put forward another common outcome metric: death. Anne T. clarified that this is currently treated as a 'PhenotypicFeature' in Biolink. The group discussed whether that makes sense or not, as 'dead' ('alive') seems more like a 'PhenotypicFeature', whereas 'death' seems more like an outcome or event. We also discussed whether outcomes could be modeled as a variant of 'exposure events'. No decisions were made, as we are planning to continue this discussion and explore other options in Biolink.

Just passing this info along to keep you informed and see if you have any thoughts to add...

nlharris commented 3 years ago

was this resolved?

karafecho commented 3 years ago

This is being actively worked on by Matt, Richard, myself, and others on behalf of the clinical data committee. Requirements gathering is complete; implementation has yet to be initiated.