Quirks and details

There are additional details that are not commonly asked but it is important to retain on record. This is a compendium of those.

• Source 1 and 9 use larger plates (1536 vs the standard 384)
  
• Source 7 and 13 are the same
  
• In JUMP-Target there is an InChIKey that maps to 2 different perturbations: ‘LOUPRKONTZGTKE-UHFFFAOYSA-N’ maps to both quinidine and quinine.
  
• The definition of controls, specially positive controls, can be tricky: Some are hard-coded in broad_babel, based on internal knowledge that was not recorded at the time of assembling the datasets. In certain datasets, such as ORF, there are additional types of positive controls: poscon_orf, poscon_cp (compound probe), and poscon_diverse.
• The treatment compounds were assayed at 10 uM at all sites, apart from source_7 where the compounds were assayed at 0.625 uM (the goal being to assay some of the compounds at a low concentration in addition to the higher concentration used for most of data production). The positive control compounds in compound, ORF and CRISPR plates were assayed at 5 uM. JUMP-Target-1-Compound and JUMP-Target-2-Compound plates were also assayed at 5 uM
• Due to some plates having letters and numbers and others only numbers, be careful when loading multiple load_data_csvs. We treat all columns and strings to avoid any potential casting issue.