EnvironmentOntology / environmental-exposure-ontology

Modular environmental exposures ontology
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ethylparabens & classification by role #10

Open cmungall opened 7 years ago

cmungall commented 7 years ago

inferred superclasses for exposure to ethylparaben:

image

are these correct?

they all come from CHEBI:

image

Our role pattern is 'has exposure stimulus' some ('chemical entity' and 'has role' some %s), so if CHEBI says that C has role R, then an exposure to C will be classified as an exposure "to" R. Is this right in all cases? Let's look.

I think we need to distinguish between

  1. classification by potentially realized roles, or rigid roles: 'has exposure stimulus' some ('chemical entity' and 'has role' some %s)
  2. classification by roles that actually realized: 'has exposure stimulus' some ('chemical entity' and 'has role' some (%s and realized-by some process))

E.g.

Should we always name these 2 classes, to avoid confusion, and for maximum precision? Also a 3rd class for when we know the role is not realized?

If we follow this pattern for 'hormone', we would have exposures to chemicals with potential hormone roles, and exposures to chemicals with realized hormone roles. The former is what most people would query by. For example, we would expect BPA to come back in a query for xenestrogen, whether or not it actually realized this role in any given exposure. Of course it's hard to determine whether in any given exposure the role is realized, so the existence of the subclass may seem odd.

It may be simplest in the short term to continue to use the uncommitted version (1), but for some cases, specifically those roles involving some kind of human intention, we make more specific subclasses.

cmungall commented 7 years ago

inference for MRE: https://github.com/cmungall/environmental-conditions/blob/eb59288ceb2421521fbbc22c85c8c1f8c0365d48/src/mapping/new-inf-mre.tsv#L48

Same kind of idea, but with drug: https://github.com/cmungall/environmental-conditions/blob/eb59288ceb2421521fbbc22c85c8c1f8c0365d48/src/mapping/new-inf-mre.tsv#L1