UHNBreast Hill Slope values are NULL in the current PDB database

[p-smirnov]

As an example, see this DDRC page: https://pharmacodb.ca/search?compound=Paclitaxel&cell_line=600MPE

If you inspect the request to PharmacoDBs graphql API, you find that for the UHNBreast experiment, the HS returned is Null. This explains why the curve is flat, and also explains why all UHNBreast curves are flat when you look here: https://pharmacodb.ca/search?compound=Paclitaxel&tissue=Breast

This could either be a PSet issue (misnamed column) or a PDI issue, but it should have been caught by PDI with an error message IMO.

[ChristopherEeles]

Issue exists in database but not in the UHNBreast PharmacoSet.

Likely due to the column name.

[ChristopherEeles]

Database query:

USE pharmacodb_test;

SELECT * FROM `profile` AS `p`
JOIN `experiment` AS `e`
ON `p`.`experiment_id` = `e`.`id`
JOIN `dataset` AS `d`
on `e`.`dataset_id` = `d`.`id`
WHERE `d`.`name` LIKE "UHNBreast";

[ChristopherEeles]

R code:

library(PharmacoGx)
library(data.table)

uhn <- downloadPSet("UHNBreast_2019")
sp <- sensitivityProfiles(uhn)
sp <- as.data.table(sp, keep.rownames=TRUE)
sp[is.na(slope_recomputed), ]

[ChristopherEeles]

R code has NA for only a subset of slope_recomputed but database query has NA for all values in the HS column.