You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
Run semsql afterwards as relationgraph will deal with the issue
Interesting: in the issue INCATools/ontology-access-kit#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 :)
This is the replacement ticket for obophenotype/upheno-dev#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: INCATools/ontology-access-kit#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)
The text was updated successfully, but these errors were encountered: