"In Clinical Trials" as a Lookup and One-hop Support Graph

[sstemann]

It looks like we are using in clinical trials for both lookups and one-hop support graphs. I think that if there is a phase 3/4 clinical trials the correct predicate to use is Treats

But we're seeing it both as a lookup (in this case by BTE https://ui.test.transltr.io/main/results?l=Sepsis&i=HP:0100806&t=0&r=0&q=1357341d-e369-463e-bb6a-6c17f7c3908d)

and as a support graph (in this case by Improving Agent https://ui.test.transltr.io/main/results?l=Crohn%27s%20Colitis&i=MONDO:0005532&t=0&r=0&q=3642d7b7-2879-4e61-99b2-6bbc78949ea4)

neither have the CT links directly

[sstemann]

adding this spawned from #846

[gglusman]

The original definition for when to make a 'treats' assertion was for "a trial that successfully passed Phase 3, or a Phase 4 trial". But, the clinical trials database has no such notion as "successfully passed", so in the Clinical Trials KG I'm relying only on presence of Phase 4 to make 'treats' assertions.

[sierra-moxon]

@gglusman - do you imagine these results from BTE also be subsumed by CTKP?
@andrewsu - does "Guppy" tag make sense here in light of the TACT discussion this morning?

[gglusman]

I am rather confused by the evidence being displayed. The lookup-edge claim is that cefazolin is in clinical trials for sepsis, and there's a 'treats' edge together with it. All the evidence displayed, though, is about product approvals from DailyMed, not a single one is from clinicaltrials (yes, I did scroll down the list):

This is a straight ingest from ChEMBL, so yes, this would be covered by CTKP. If there are phase 4 trials as suggested, there will be a 'treats' assertion already present in the KG.

[sierra-moxon]

Discussed CTKP in TACT today and there will be a push to harmonize CTKP ingests (vs. Chembl/others) in the next sprint.
@andrewsu - maybe the only change with that would be that we'd see the "in clinical trials" edge from CTKP as a support to a "treats" assertion from BTE. (I know we're planning on hearing from CQS folks next architecture meeting - another reason to move this to hammerhead).

[andrewsu]

Looks like the desired behavior is being observed (at least on test):

• UI: https://ui.test.transltr.io/results?l=Sepsis&i=HP:0100806&t=0&r=0&q=83d93e4a-2a96-447c-af63-0211cb8f55d0
  

• ARAX UI: https://arax.ci.transltr.io/?r=a0a10664-0386-427f-a0c5-a99194cabbc5
  
  support graph:
  

I think this satisfies the "ask" of BTE, but let us know if not!

[gglusman]

@andrewsu That 'in_clinical_trials_for' support edge comes from ChEMBL, not from CTKP. I'm not sure this answers Sierra's ask.

[andrewsu]

@gglusman I interpreted this issue as primarily about the structure of the treats and in_clinical_trials_for edges. But yes, you're right, the source of these edges (CTKP vs chembl) is also mentioned here. Is the Automat CTKP already available in the ITRB environment? It looks like the smartAPI annotation only shows a non-ITRB dev instance. If that's right, I suggest we close this issue and leave the data source swap for a different issue, synced with the next sprint.

[gglusman]

The Plover CTKP will be available in ITRB/CI next Friday.

[andrewsu]

Just so we can separate the two topics here, I'm going to close this issue that is primarily about the structure of results, and I created a new issue to track the swap of data sources for in_clinical_trials_for edges. Please let me know if that doesn't fully address the concerns!