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monarch-initiative / monarch-semantic-similarity-profiles

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Provide make goal for upheno2-merged.owl #8

Closed matentzn closed 1 year ago

matentzn commented 1 year ago

This is the replacement ticket for https://github.com/obophenotype/upheno-dev/issues/38

We need to iterate over this goal, as it is, as of yet, not clear how to fix this. In the old uPheno,

MP:123 = HP:123.

In uPheno2, MP:123 sub UPHENO:111, HP:123 sub UPHENO:111, so the equivalence axiom is replaced by a common parent. This drastically changes the way (graph-based) semantic similarity algorithms behave.

This is the key ticket: https://github.com/INCATools/ontology-access-kit/issues/634

@souzadevinicius This has a high priority, but right now, I don't know how to advice you on fixing it.

Can you make sure this does not fall under the radar, and mention it to me every time we meet? (add to your board as high priority)

matentzn commented 1 year ago

I think we have a solution now:

  1. change mapping predicate to owl:equivalentClass
  2. Run semsql afterwards as relationgraph will deal with the issue

Interesting: in the issue https://github.com/INCATools/ontology-access-kit/issues/634 explains an hypothesis that actually children of equivalent classes will move closer together in the semantic space, which may introduce a bias. Ask me about this @souzadevinicius if you want to understand better :)

matentzn commented 1 year ago

Did this work? Do you see significant differences in the upheno2-lattice and upheno2-equivalence profiles?