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Include subsumer classes in Exomiser output #17
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@caufieldjh how far are you going with this exomiser work? We are doing a lot of the same things now - especially setting up these comparative experiments etc. If you continue investing in things like converting OAK semantic similarity profiles to Exomiser tables, then we absolutely should add this to the ETL preprocessing in pheval rather than here.. |
This isn't the OAK semantic similarity, it's a faster implementation that can be part of the usual Monarch KG build. If that essentially mean "run it through Pheval" then that's entirely doable, but for now we have a few different use cases and one of them is just seeing if we're improving on existing phenodigm scores. That use doesn't really require a whole ETL pipeline. In the slightly longer term though, sure, it can absolutely be used in the course of building Pheval comparisons. |
I don't care that much if it's going through oak, but it should export the oak semantic similarity format, not some custom table. In any case, this is all too close to home - We have a concrete mandate to implement what you are doing in PhEval, and I am more than happy for you to implement it, but we need to coordinate the code a bit - for now the most important thing is that semsim exports the standard semantic similarity profile format Chris defined, and I thought this was on someone's priority list? Is there any way I can get a complete description of where your task starts and where it ends? What are you testing, tuning etc and what is the exact goal? |
Exomiser format looks like this:
With columns being subject, object, Jaccard, Resnik, and subsumer, in that order.
We would like to include something like this subsumer column in the output, with the knowledge that it may always or nearly always be a Upheno node.
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