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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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no results at all #678

Closed gglusman closed 2 months ago

gglusman commented 9 months ago

Re-testing what drugs may treat EDS vascular type I get exactly zero results, which is kind of surprising. Term matching worked fine. The query was submitted and returned the final 'No results available.' within less than one minute. Checked the pk via ARAX interface, and saw that the TRAPI return was empty from multiple sources.

image
sierra-moxon commented 9 months ago

retested this morning in TAQA, still seeing empty results for this disease. Sharat - we tried running all the rare disease through a big test and we haven't seen this disease in the results. Bill - there are 30 subtypes in MONDO, so its likely we may not have results on all the subtypes

we know there is a UI suggestion to group. maybe group by disease grouping classes, then we'd see more.

Bill - It might be nice if the UI saw that the more general answer has results and to query for the more generic one.
Sui - the more generic disease does return results from SPOKE. In general, it would be worth it to look higher up in the hierarchy but we don't do this. Vlado - we had implemented going up the hierarchy but it returned too many spurious results. Sui - treat symptoms not diseases but no nominal therapy associated with that. complex treatment strategies are hard to capture.

Group thinks we should close this ticket as "we don't have results for this specific disease".

sierra-moxon commented 9 months ago

Casey - we can add a test asset for this case - e.g. document some expected responses to this query and we can add it to the test assets for P/F tests.

@gglusman - do you think you could provide a set of expected results and then I can get it into assets. Bill - a generic message for no results to try a higher level term would be good too as a general solution.

sharatisrani commented 9 months ago

Clarification - ran an E-D query, saw 893 results for 6 E-D subtypes, from all ARA's, but this was not one of the subtypes. Thus probabilistically there are many subtypes for which we can expect no results

gglusman commented 9 months ago

Upon retest on 2024/1/23 I get hundreds of results.

Peeking at it on ARAX interface while it's still waiting for new results according to the UI, I see: image The error for imProving Agent is 'empty TRAPI response'. All other ARAs already returned results, but the UI still shows pending status. ...while I was typing this I kept re-checking, and eventually it declared that no more results were expected. But this was quite long after processing was done according to ARAX interface.

Editing to add: robokop's response is marked as 'non-TRAPI' image

gprice1129 commented 8 months ago

@gglusman current the ARAX UI does not use the merged ARS result as far as I know. The Test UI does use the ARS merged result. We've found this adds a significant amount of time to get results back, most likely because the message size is very large.

edeutsch commented 8 months ago

ah, this is an interesting point that I hadn't considered before. As far as I'm aware when you specify a "parent pk" to the ARAX GUI, it asks the ARS about it and gets back a list of "children", which are all the individual responses that you see above in the screen shot. The ARAX GUI then retrieves all the individual children and that's what you see.

I think the latest poster is correct that the ARS-merged result is not provided as a child of the parent pk and thus is not available to the ARAX GUI. Therefore it is not possible currently to view in the ARAX GUI the exact TRAPI that the main UI is working with?

So perhaps a question for @MarkDWilliams or @ShervinAbd92 : can/should the ARS-merged result TRAPI be listed as a child of the parent PK, so that we can view the final merged TRAPI in the ARAX UI? or is that already available somehow and we need to teach the ARAX GUI how to access it?

ShervinAbd92 commented 8 months ago

Hi @edeutsch Yes, I believe we can add the last merged_pk as a child to the parent PK. However, is this an urgent request? we can do it next week.

edeutsch commented 8 months ago

Thanks @ShervinAbd92 I do not view this as very urgent, so next week would be fine with me, but others may chime in with different priority views. thanks!

gglusman commented 8 months ago

Right now, getting no results for what drugs may treat CAS (on CI). Peeking at the pk on ARAX UI, I see hundreds of results. Interestingly, fewer agents than usual are listed: image

ShervinAbd92 commented 8 months ago

Hi @gglusman yes so i implemented adding the merged data as a child of parent pk and if you look into the https://ars.ci.transltr.io/ars/api/messages/ u can see all the agents (ARAs and KPs) are showing up but not on the GUI, I already notified Luis Mendoza about it and he will help us debug next week when he comes back from vacation.

sierra-moxon commented 5 months ago

@ShervinAbd92 - should this be closed as completed now? :)

ShervinAbd92 commented 5 months ago

Yes @sierra-moxon this has been implemented for a while

gglusman commented 4 months ago

I'm observing this again - the 'no results' outcome. What drugs may treat Alzheimer's Disease Via ARAX interface I see there are 500 results from BTE, and 126 from Unsecret (though it indicates error 500), yet the UI shows nothing.

gprice1129 commented 4 months ago

@gglusman we are currently seeing no results on Production from any query. On the ARAX interface you need to look at the ars-ars-agent (merged results) to understand why. There is currently some issue with the TRAPI validator that causes the ARS to send back 422 errors for any merged results, thus causing the UI to not show anything.

@ShervinAbd92 is working on it.

ShervinAbd92 commented 2 months ago

this issue has been resolved.