Indicate number of unmatched phenotypes per column

[jmcmurry]

This is really more of an owlsim / scigraph issue but manifesting here.

It is not clear why we're seeing higher scores for diseases that have fewer phenotype matches. I expected this to be the result of slightly different scoring, or weighting by IC score, but this appears not to be the case?

@kshefchek @jnguyenx ?

[jnguyenx]

Scoring is done by the owlsim server. @cmungall must have answers for that.

[cmungall]

we have an option to show unmatched phenotypes for the query, but not for the matches. If we did, you'd see the lower scoring ones would have many unmatched phenotypes

[jmcmurry]

Ah right; of course. Perhaps then, phenogrid could at least have a number for each column showing how many unmatched phenotypes there are? That would help make more sense of reports like this.

[mellybelly]

I've always disliked the hidden unmatched terms. If we implement a hierarchical y axis there might be a way to render them differently rather than hiding them

[jmcmurry]

On a related note, when we get to phenogrid from a disease page (compare tab) I can't figure out why it is that the top disease hit isn't either:

A) a different disease altogether
OR
B) the same disease as the query disease but scoring a 100% profile match

We have neither A nor B now: the top hit is always identical in name/ID to the disease that spawned the query; however the match scores can be well below 100; for example https://monarchinitiative.org/disease/OMIM%3A127750#compare has a match score of 79. What am I missing?

[cmungall]

In this case, what is in owlsim doesn't match what is in solr. This is odd as the owlsim data is dumped directly from golr. It could be a data synchrony issue, or it could be something wrong with the golr-exporter script. @jnguyenx and @kltm can explore more tomorrow.

[cmungall]

Checked on beta, same issue. But it also showed odd fly matches.

Following up, we should not be including inferred phenotypes like these
https://beta.monarchinitiative.org/gene/FlyBase:FBgn0040074

(this belongs in a separate ticket, just noting here for now)

EDIT: not a phenogrid issue, now tracked here: https://github.com/monarch-initiative/monarch-app/issues/1243

[yuanzhou]

Let me know if there's any changes better to be made in Phenogrid, or just help with testing.

[harryhoch]

@yuanzhou, don't worry about this for now.