search

NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
7 stars 0 forks source link

Allow users to exclude and/or compare lists of entities #55

Open karafecho opened 1 year ago

karafecho commented 1 year ago

The QotM surfaced SME desire for functionalities to compare and exclude lists. This is under active discussion in the Ops & Workflows WG, but it is also relevant to the UI work. See https://github.com/NCATSTranslator/OperationsAndWorkflows/issues/77.

karafecho commented 1 year ago

Also see: https://github.com/NCATSTranslator/testing/issues/227.

capasfield commented 1 year ago

Actively being discussed in Ops and Workflow.

sierra-moxon commented 1 year ago

from TAQA: this should not be reviewed again in TAQA

dkoslicki commented 1 year ago

Per the operations and workflow (O/W) meeting Jan. 10th, O/W will not be implementing this functionality. The ability to exclude things is on the TRAPI radar per this pull request by @edeutsch. Other light-weight set operations (union, intersection, difference of result sets) will be handled at the UI level and/or user level after UI data export is operational.

gprice1129 commented 1 year ago

@karafecho the UI team would like to get clarification on what exactly is being requested. Examples would be extremely valuable!

karafecho commented 1 year ago

Sure thing, @gprice1129. Several SMEs and the TCDC have identified use cases where it would be helpful to be able to exclude and/or compare entities within two lists.

Here's an example from the QotM: https://github.com/NCATSTranslator/testing/issues/220 and https://github.com/NCATSTranslator/testing/issues/227. In this example, the SME wanted to compare two lists of genes and identify those genes that are shared by both lists and those that are unique to one or the other list.

Here's an example from the TCDC: https://github.com/NCATSTranslator/Clinical-Data-Committee-Tracking-Voting/tree/main/GetCreative()_DrugDiscoveryRepurposing_RarePulmonaryDisease/Path_A. In this example, the TCDC wanted to identify chemical entities that are not in the first set of chemical entities but that act on the same gene set. Here, we were using an exclude edge, which only ARAX currently supports and is no longer planned for implementation via Operations & Workflows, as David K. points out above.

gprice1129 commented 1 year ago

@karafecho thank you! Currently the UI team is working to understand the possible user impact and effort required to make this happen. We will comment on the ticket soon with an update on the status for this release cycle (or possibly just because we need further clarification).

jh111 commented 1 year ago

Here is another example from a SME Question of the Month. What drugs may treat Psoriatic Arthritis, excluding drugs that are known to treat Psoriasis. Note the issues of may treat vs treats and the issue of known vs not known are somewhat orthoganal to the issue of exclusion, but I wanted to put in the specific SME scenario for context.

sierra-moxon commented 5 months ago

@gprice1129 - do you see this as an implementable issue in the next year?

If not, I would propose closing it here, and instead adding the request to the TACT parking lot for future development effort.

gprice1129 commented 5 months ago

@sierra-moxon this is on our radar but I'm not sure when we will implement yet.