Test Results Node - MVP1 - No Description

[sstemann]

Looks like we lost the result node description on MVP1 results. The descriptions are showing for MVP2 results, but I'm not seeing them on What drugs may treat (in Test 7/14):

Sneddon Syndrome:

Meniere Disease

Familial Pityriasis Rubra Pilaris

May be related to #112

[dnsmith124]

I don't see any issue with the data on the FE in these examples (meaning there's no description data that the FE is failing to display).

This is likely an attribute server issue, but I'll let @gprice1129 confirm.

[newgene]

Yes, pending on this MyChem.info issue we are working on right now: https://github.com/biothings/mychem.info/issues/159

[sstemann]

@newgene will this be resolved by the 8/18 code freeze?

[newgene]

@sstemann yes, that's our plan.

[newgene]

@sstemann just fyi we have completed this dependency issue at https://github.com/biothings/mychem.info/issues/159. @MarkDWilliams and @Genomewide's teams are working on the integration with the ARS and UI.

[sstemann]

@newgene i'm not sure if i'm testing this right but i have results from the Prod UI for MVP1 Maturity-onset Diabetes Of The Young

https://ui.transltr.io/main/results?l=Maturity-onset%20Diabetes%20Of%20The%20Young&i=MONDO:0018911&t=0&q=4231e8a1-4ae4-4f4f-9b5e-53774698655b

and some of the tops results dont have descriptions, if I'm doing this right in annotator, then I'm guessing its because its not available?

Insulin detemir - No description in the UI

UI Links to https://pubchem.ncbi.nlm.nih.gov/compound/16137271 No definition in the annotator: https://biothings.ncats.io/annotator/PUBCHEM.COMPOUND:16137271?fields=unii.ncit,chebi.definition

Then if i find one that's Chebi like Uric Acid

There's no description, but here's what the UI LInks out to: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27226 And what the annotator has on it https://biothings.ncats.io/annotator/CHEBI:27226?fields=unii.ncit,chebi.definition

But that definition "An oxopurine that is the final oxidation product of purine metabolism." isn't showing up in the UI.

So it looks like there are some substances without descriptions and some with definitions that aren't in the UI, is that right?

Is this by design?

[newgene]

UI Links to https://pubchem.ncbi.nlm.nih.gov/compound/16137271 No definition in the annotator: https://biothings.ncats.io/annotator/PUBCHEM.COMPOUND:16137271?fields=unii.ncit,chebi.definition

I checked the above case, looks like the root reason is because the record of PUBCHEM.COMPOUND:16137271 in MyChem.info is not linked with the record of UNII:4FT78T86XV. That unii record includes the mapping to NCIT id of C65920, which allows us to get the drug description from NCIT. We will take a closer look of this issue at MyChem.info side at https://github.com/biothings/mychem.info/issues/169.

[gprice1129]

The definition of done for this ticket is extremely unclear. I suggest we close this ticket and open up "No Description" tickets for individual results/nodes. If not singular at least a finite number.

[Genomewide]

@newgene, how often do we expect to have a description, and when should we expect not to have a description?

[newgene]

@Genomewide @gprice1129 this issue has been fixed upstream in the first new release of MyChem.info in 2024 :-)

This issue https://github.com/biothings/mychem.info/issues/169 has been closed.

I have verified NCIT description now returned from the annotator:

https://biothings.ncats.io/annotator/CHEBI:27226?fields=unii.ncit,chebi.definition

[sstemann]

i get a little confused - there are still no descriptions sometimes. in TEST UI:

https://ui.test.transltr.io/main/results?l=Ehlers-danlos%20Syndrome,%20Vascular%20Type&i=MONDO:0017314&t=0&r=0&q=4b7cd9bb-3154-4257-867f-ffcb26d23d6c

@Genomewide

[gprice1129]

@sstemann we will be looking into descriptions this cycle.

[sstemann]

@gprice1129 i think on 3/27 release their were some bullets about annotation server just noting here i'm still seeing sparsity on these descriptions:

https://ui.test.transltr.io/main/results?l=Exotropia&i=MONDO:0001286&t=0&r=0&q=0b2a500e-a935-4191-9f39-7ade0e25ce83

https://ui.test.transltr.io/main/results?l=Apidra&i=PUBCHEM.COMPOUND:16136701&t=3&r=0&q=73bce986-35eb-4bb3-92f3-e2fc28e7464e

[gprice1129]

@sstemann this is on our radar but was not part of the annotation work we did.

[gaurav]

This probably won't be super helpful here, since I think you're mainly talking about genes and chemicals which we don't have descriptions for yet, but NodeNorm now returns descriptions for CURIEs in Ubergraph, such as UBERON:0003684:

{
  "UBERON:0003684": {
    "id": {
      "identifier": "UBERON:0003684",
      "label": "abdominal cavity",
      "description": "The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity)."
    }, ...
  }
}

We only get our descriptions from Ubergraph at the moment, so only ontology CURIEs can have descriptions. But if there's a source of descriptions we can ingest we'd be happy to do that.

[sstemann]

still a problem: https://ui.test.transltr.io/main/results?l=Sneddon%20Syndrome&i=MONDO:0008436&t=0&r=0&q=80e2fc7c-f372-4438-ba0e-82707af60b15

[sstemann]

still no descriptions on this MVP1 : https://ui.test.transltr.io/main/results?l=Sneddon%20Syndrome&i=MONDO:0008436&t=0&r=0&q=05421421-a30e-4f28-8e5c-8a0312be0e2a

[sierra-moxon]

@sstemann - I believe this is fixed or otherwise I can not find results without descriptions in the first several pages of returns today for the query above.

I did notice a discrepancy in the view w/re to descriptions though, and its not clear to me why? -- for example: Verapamil has a description without opening the results, but the other two chemicals in this result appear to not have descriptions:

however, when I "open" the results without the descriptions, I do see the descriptions after all:

Is this the issue we're trying to solve or can we close this as complete?

[dnsmith124]

@sierra-moxon Based on user feedback the UI team determined that the chebi role tags on results are more important than the description, so if any are present they bump the description down "below the fold" so to speak.

That's not the issue this ticket was concerned with though, so I believe we can close!