24.03 docs and comms

[buniello]

Ahead of Platform/PPP 24.03 release, we will have to update/build the following documentation pieces:

• [x] Direction of effect - Juan and PU
• [x] New uploads functionality with new screenshots for PPP - PU
• [x] New pharmacogenetics data - AB
• [x] Pharmacogenetics in safety - IL
• [x] New Project Score - DS
• [x] AOTF API playground release notes - PU
• [ ] iFuncOnc OTAR2061 - SYH, AB, DS
• [x] Release comms - HC
• [x] Release notes - PU
• [x] Platform documentation citation updates - PU
• [x] ChEMBL Safety - PU
• [x] PPP release notes

[ireneisdoomed]

April from EVA and I would like to write a blogpost to introduce the PharmGKB data, if that is of any interest @HelenaCornu

[HelenaCornu]

Always! Do you think you can have a draft ready in ~1 month? Then we could publish it for the release

[HelenaCornu]

@ireneisdoomed Please could I have the following metrics for the blogpost? Just confirming exact numbers for some of the things mentioned in the team meeting:

• How many associations in the Platform have a direction of effect assessment? (David mentioned 800,000)
• You mentioned that there are ~1000 targets with known adverse events, half come solely from pharmacogenetics evidence. Do you have the exact numbers for this?

Thank you! 🚀

[ireneisdoomed]

@HelenaCornu

1. 2,871,198 of evidence with an assessment. Breakdown:

   (
   evd.filter(
       (f.col("directionOnTrait").isNotNull()) | (f.col("variantEffect").isNotNull())
   )
   .groupBy("variantEffect", "directionOnTrait")
   .agg(
       f.count("*").alias("count"),
       f.collect_set("datasourceId").alias("datasourceIds"),
   )
   ).orderBy("variantEffect").show(truncate=False)
   +-------------+----------------+-------+----------------------------------------------------------------------------------------------------------------+
   |variantEffect|directionOnTrait|count  |datasourceIds                                                                                                   |
   +-------------+----------------+-------+----------------------------------------------------------------------------------------------------------------+
   |null         |risk            |399749 |[eva, orphanet, intogen, ot_genetics_portal, gene2phenotype, eva_somatic, cancer_gene_census]                   |
   |null         |protect         |202008 |[eva, ot_genetics_portal, chembl, eva_somatic]                                                                  |
   |GoF          |risk            |70354  |[orphanet, intogen, ot_genetics_portal, gene2phenotype, cancer_gene_census]                                     |
   |GoF          |protect         |141128 |[ot_genetics_portal, chembl]                                                                                    |
   |LoF          |risk            |1437593|[impc, eva, orphanet, intogen, ot_genetics_portal, gene2phenotype, gene_burden, eva_somatic, cancer_gene_census]|
   |LoF          |null            |41034  |[eva, ot_genetics_portal, gene_burden, eva_somatic]                                                             |
   |LoF          |protect         |579332 |[eva, ot_genetics_portal, gene_burden, chembl]                                                                  |
   +-------------+----------------+-------+----------------------------------------------------------------------------------------------------------------+

2. 932 targets with known liabilities.
   • Data from PGX for 541 targets
   • 429 of them as the only source