search

clinical-biomarkers / biomarker-issue-repo

Issues repo for the biomarker team.
0 stars 0 forks source link

Biomarkers with Negative Score #25

Open DaniallMasood opened 1 week ago

DaniallMasood commented 1 week ago

Biomarkers with negative score should be marked and denoted with a red banner on the biomarker entry page.

@sujeetvkulkarni what is the best way to do this?

sujeetvkulkarni commented 1 week ago

@seankim658 is negative value important? Can you make them all from 0 and above by adding a weight or something?

DaniallMasood commented 1 week ago

@sujeetvkulkarni yes negative score is important for us. Not all biomarker entries are viewed and are given -1. Some entries are not complete biomarkers and are given -2 score. 0 score is assigned to biomarkers for generic conditions (eg, "cancer")

sujeetvkulkarni commented 1 week ago

@DaniallMasood oh ok got it. We can highlight it on list page in some way, either we can highlight link to biomarker page or score value as red or something. Based on your preference.

DaniallMasood commented 1 week ago

@sujeetvkulkarni i think highlighting score value would be great. is it possible to also highlight the "Biomarker Details for XXXXXX" red on the biomarker entry page as well?

sujeetvkulkarni commented 1 week ago

@DaniallMasood If you can add the score value in details page api. We can do it.

DaniallMasood commented 1 week ago

@seankim658 can you do this? -1 for all ClinVar and -2 for SenNet?

seankim658 commented 1 week ago

The scores are already on the details API response under the key score. Technically on the list endpoint on the backend I just rename the key from score to hit_score before returning the response because originally we needed the API response to match the GlyGen list response as close as possible. However, in the database it is stored as score since our concept of a score isnt exactly a hit score like GlyGen's score concept is. I'm not sure if we also want to rename the search results page column to just score but Daniall can decide on that.

Right now we do not have the negative scored biomarkers in the database yet, they will get pushed in the next data push.

seankim658 commented 1 week ago

But everything on the backend is in place to implement this. From what I understood when Raja explained it, should just check the score less than 0 and then just have a small red banner with some text on the detail page. @DaniallMasood can provide the text. And then I'm not sure how you want to format the search results page whether that should have anything for the negative scores.

DaniallMasood commented 1 week ago

@sujeetvkulkarni @seankim658 yeah we can do a red banner on the top right of the biomarker entry page and the text can be "Pending Review"

sujeetvkulkarni commented 1 week ago

@DaniallMasood we can do this change but I think it will be best if we do this when data is available, so we can test it. Just let me know on this ticket when the data is pushed.

DaniallMasood commented 1 week ago

@sujeetvkulkarni that is fine

@seankim658 will the data be pushed tomorrow with the negative scores?