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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.

Home Page:https://obophenotype.github.io/upheno/

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create a pattern for biological attribute severity

Daniel-Olson opened this issue · comments

commented

This pattern is meant to describe the severity of biological attributes. Our use case is related to outcomes of clinical outcomes assessments where rank of severity is pertinent. We would also like to include a pattern for the 'normal' quality of a biological attribute.

We are using the patterns:

  1. Abnormal -
    equivalentTo:
    text: "'has_part' some (%s and ('has_modifier' some ('abnormal' and ('has_modifier' some %s))))"
    vars:
  • attribute
  • severity
  1. Normal -
    equivalentTo:
    text: "'has_part' some (%s and ('has_modifier' some 'normal'))"
    vars:
  • attribute

@nicolevasilevsky @matentzn

commented

@rays22 this is important also for issue #903. This asks for two modelling issues:

  1. Using "severity" modifiers on the "abnormal" modifier. The question here is if "has modifier" is the appropriate relation - I think it could be, but something more specific, like "has degree of intensity" could be an option as well.
  2. The use of OBA attributes in place of the post-composed "Q inheres in some E" expression.

Let me know what you think, I think it makes sense, but maybe I am not seeing everything clearly.