how to summarize a path with passive form predicate?

[dkoslicki]

Having the paths always go left to right leads to awkward paths like: Abat "Has Decreased Activity Or Abundance Caused By" Ube2c "Has Increased Expression Caused By" Valproic Acid instead of the simpler: Valproic acid "increases expression of" Ube2c "decreases activity or abundance of" Abat.

[sandrine-m]

@dkoslicki I think this issue is related with other issues on the template "which gene is upregulated by Valproic acid" (please correct me if I am wrong. Here is the same template in CI: PK : fb4a9557-4271-4531-8a4f-a11128c76587

It looks like the issue you are describing is fixed. Could you please validate and close the ticket if so or specify (PK, screenshots...etc. )?

Thank you so much!

[dkoslicki]

Hmmm... it appears to me to still be there. Reading the paths is still in the form: Abat "Has Decreased Activity Or Abundance Caused By" Ube2c "Has Increased Expression Caused By" Valproic Acid.

Note: this is not a bug, but feedback that this is kind of awkward. But if the UI team disagrees, that's ok (I recall a design decision always have paths go left to right, or something like that).

My suggestion is to flip the entire path: Valproic acid "increases expression of" Ube2c "decreases activity or abundance of" Abat or flip the edge directions (abat)<-[decreases]-(Ube2c)<-[increases]-(Valproic acid)

[sandrine-m]

Oh! I see! This is not a UI display issue then it is more of an ARA right? "how to summarize a path with passive form predicate?" Would it be ok I rename it? added "reasoning" label and triage into answer quality

[dkoslicki]

Actually, @Genomewide mentioned at the relay it was a UI thing. Arrow direction is switched by the UI to make everything left to right, this changing the phrasing ov the displayed predicates

[gprice1129]

User testing is required to determine the correct action for this issue.

[dkoslicki]

@sandrine-m

"how to summarize a path with passive form predicate?"

I think that is a more accurate title!

[Genomewide]

I think that David and Gus are right here. It is awkward and we do need to test it, but we should review this ASAP.
The difference here is that the drop-down question has the trailing 'by'. So, the question is actually structured differently and the answers probably should be as well.

[sandrine-m]

@dkoslicki I changed the title and I will create a label for this type of issue. All, please tell me if you agree.

I understand we have 2 issues here:

1. UI-display: when the templates:
   • what gene is upregulated by [compound]
   • what gene is downregulated by [compound] This is not a question of arrows direction. The issue is that paths in results should be displayed starting from [compound] so that results are displayed in the non-passive form that is more intuitive for user (due to the presence of "by" in the question.
2. Reasoning: in this particular example, when we ask the question What gene is upregulated by Valproic Acid? We get the first result "ABAT". If we look at the explaination for this result we get what David was first explaining: Valproic acid "increases expression of" Ube2c "decreases activity or abundance of" Abat._ ABAT is not the answer but UBE2C is. Note that UBE2C never shows up as a result. This looks like a specific case of "opposite of what I asked for" where questions are in the passive form. Adding corresponding issue labels.

[sierra-moxon]

@Genomewide @gprice1129 - has any user testing been done on this issue or shall we close it as "won't do" ?

[sstemann]

any updates on if this is going to change? @dnsmith124

[dnsmith124]

@sstemann this is not planned to be addressed before the end of the funding period.