NCATSTranslator/Feedback

Add HPO to the choices for MVP1 "What drugs may treat"

sstemann opened this issue · 10 comments

sstemann commented

We'll need to develop a query block list for HPO phenotypes

gaurav commented

Thanks! I'm tracking this on NameRes at TranslatorSRI/NameResolution#93.

I think the best way to do this might be to check the previous blocklist terms we identified in TranslatorSRI/NameResolution#63 against NameRes, but filtering to MONDO and HPO (i.e. query for https://name-lookup.ci.transltr.io/lookup?string=Suicide&offset=0&limit=10&only_prefixes=MONDO%7CHP and decide if we want to block the resulting term, HP:0031589 "Suicidal ideation").

gprice1129 commented

@gaurav is this a UI, NameRes or both issue?

Genomewide commented

For us,I think it is just adding the curie prefix to the possible ones that are returned. So, MONDO and HPO can be returned.
@gaurav We can 'OR' curry prefixes right?

After that, there will need to be testers trying to break it.

I also think we can help by showing something similar how the Monarch site does by indicating wether a term is a 'disease' or 'phenotype'

dnsmith124 commented

@Genomewide @sstemann do we want to enable HPO immediately, or wait for the blocklist to be implemented?

sstemann commented

@Genomewide @dnsmith124 i would like to defer HPO being deployed to production until the blocklist is identified and implemented. I think the draft plan for the UI is:

  • Add back the ability of the autocomplete to return HPO curries.
  • Enlist testers (yet unidentified) to do some searches looking for terms to be blocked or possibly confusing terms when displayed with diseases from MONDO.
  • Individual terms deemed inappropriate may be blocked using the block list.
  • Terms that appear duplicative or confusing for other reasons will need specific consideration for how to deal with them.
  • The Monarch initiative has both and simply indicates in the same row of an answer whether it is a phenotype or a disease. We currently plan to adopt this as well.
dnsmith124 commented

@sstemann HPO terms have been added to the autocomplete for Drug/Disease queries and I can confirm they're showing up on CI! We can begin testing for the blocklist now.

I still need to add some additional design elements that make whether you're selecting a disease or a phenotype clear to the user, I'm working on that now, but I didn't want that to hold back testing.

dnsmith124 commented

I've added an icon and textual indication of what biolink type an autocomplete term is to the autocomplete window. The change is live on CI, so I believe the UI's work on this ticket is complete.

gaurav commented

I've gone through the list of red team terms we found two Relays ago and tested them against HPO in https://github.com/NCATSTranslator/Blocklists/milestone/1. I plan to review them in TAQA tomorrow, get Link Brokers to okay the final list, and then implement it in NameRes Dev.

sierra-moxon commented

Per discussion offline, we want to implement HP in the autocomplete in the next release and also finalize the blocklist.

sstemann commented

in prod as of 2/27