Enhance drug sensitivity data with compound metadata

[allisonvuong]

@tfkillian , @lgatto , the depmap_drug_sensitivity() data is very useful, but it currently omits the metadata on the compound, which is an internal broad identifier.

> dr <- depmap::depmap_drug_sensitivity()
snapshotDate(): 2021-02-07
see ?depmap and browseVignettes('depmap') for documentation
loading from cache
> dr
# A tibble: 2,708,508 x 4
   depmap_id  cell_line             compound                         dependency
   <chr>      <chr>                 <chr>                                 <dbl>
 1 ACH-000001 NIHOVCAR3_OVARY       BRD-A00077618-236-07-6::2.5::HTS    -0.0156
 2 ACH-000007 LS513_LARGE_INTESTINE BRD-A00077618-236-07-6::2.5::HTS    -0.0957
 3 ACH-000008 A101D_SKIN            BRD-A00077618-236-07-6::2.5::HTS     0.379
 4 ACH-000010 NCIH2077_LUNG         BRD-A00077618-236-07-6::2.5::HTS     0.119
 5 ACH-000011 253J_URINARY_TRACT    BRD-A00077618-236-07-6::2.5::HTS     0.145
 6 ACH-000012 HCC827_LUNG           BRD-A00077618-236-07-6::2.5::HTS     0.103
 7 ACH-000013 ONCODG1_OVARY         BRD-A00077618-236-07-6::2.5::HTS     0.353
 8 ACH-000014 HS294T_SKIN           BRD-A00077618-236-07-6::2.5::HTS     0.128
 9 ACH-000015 NCIH1581_LUNG         BRD-A00077618-236-07-6::2.5::HTS     0.167
10 ACH-000018 T24_URINARY_TRACT     BRD-A00077618-236-07-6::2.5::HTS     0.832

The relevant associated metadata appears to be in file: primary-screen-replicate-collapsed-treatment-info.csv. Is this something you would consider merging and serving?

> md <- read.table("primary-screen-replicate-collapsed-treatment-info.csv", sep=",", quote='\"', header=TRUE, comment.char="")
> head(md)
                                  column_name               broad_id       name
1 BRD-A00055058-001-01-0::2.325889319::MTS004 BRD-A00055058-001-01-0    RS-0481
2         BRD-A00842753-001-01-9::2.5::MTS004 BRD-A00842753-001-01-9 oleuropein
3         BRD-A02232681-001-01-8::2.5::MTS004 BRD-A02232681-001-01-8 isoleucine
4         BRD-A04447196-001-01-8::2.5::MTS004 BRD-A04447196-001-01-8  gepefrine
5  BRD-A04971881-003-01-3::2.65294603::MTS004 BRD-A04971881-003-01-3 cloranolol
6         BRD-A08316590-001-01-3::2.5::MTS004 BRD-A08316590-001-01-3 broxaterol
      dose screen_id                            moa
1 2.325889    MTS004                immunostimulant
2 2.500000    MTS004      estrogen receptor agonist
3 2.500000    MTS004                           <NA>
4 2.500000    MTS004    adrenergic receptor agonist
5 2.652946    MTS004 adrenergic receptor antagonist
6 2.500000    MTS004    adrenergic receptor agonist
                             target disease.area  indication
1                              <NA>         <NA>        <NA>
2                             GPER1         <NA>        <NA>
3 ACADSB, BCAT1, BCAT2, IARS, IARS2         <NA>        <NA>
4                              <NA>   cardiology hypotension
5               ADRB1, ADRB2, ADRB3         <NA>        <NA>
6                             ADRB2         <NA>        <NA>
                                                                 smiles
1                                CC(NC(=O)C1CSCN1C(=O)c1ccccc1)c1ccccc1
2 COC(=O)C1=COC(OC2OC(CO)C(O)C(O)C2O)\\C(=C/C)C1CC(=O)OCCc1ccc(O)c(O)c1
3                                                      CCC(C)C(N)C(O)=O
4                                                     CC(N)Cc1cccc(O)c1
5                                        CC(C)(C)NCC(O)COc1cc(Cl)ccc1Cl
6                                             CC(C)(C)NCC(O)c1cc(Br)no1
     phase
1  Phase 2
2  Phase 2
3 Launched
4 Launched
5 Launched
6  Phase 3

[tfkillian]

@allisonvuong I will try to work in the compound metadata for the drug dependency data with the next update.

[tfkillian]

The primary-screen-replicate-collapsed-treatment-info.csv metadata has been added to the latest version of the drug dependency data. @lgatto you can close this issue

[allisonvuong]

Great, thanks so much @tfkillian! When will this be merged into master?

[lgatto]

Merged into master now. I will push to Bioc later today.