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Graph Context for Complex Phenotype Classes

Background

We created a set of complex phenotype terms in CPONT such as CPONT:0000029 ("abnormal knee joint functionality, severe intensity").

These complex terms are defined by a combination of

  1. a severity term from PATO (e.g., PATO:0000396, "severe intensity"), and
  2. an attribute term from OBA (e.g., OBA:2060187, "knee joint functionality").

In the knowledge graph representation of the node for this complex class however, the OWL logic defining it in terms of those other two components is lost. In the graph, the context for each term then is just whether it is as subclass of "severely affected phenotype", or "moderately effected phenotype", or "normal phenotype", which is useful in certain cases but doesn't capture any of the semantic info from the original OBA term.

Questions

  • Would it make sense to materialize the edge from CPONT:0000029 to OBA:2060187 in CPONT, for example?

  • If we did that, should we also materialize the edge from CPONT:0000029 to PATO:0000396?

  • Do we need to also worry about potential missing relationships between HPO terms in CPONT, and these new complex classes? For example, what if the new phenotype described by the PATO severity and OBA attribute actually looks like it should fit in the hierarchy underneath HP:0000152 "Abnormality of the head or neck"?

I'm wondering if the answer to these questions might also be impacted by how frequently we will be created new, not-imported, complex classes?