Generate drug index with the new chembl release 28

[mkarmona]

Few things changed from the previous release so better to double-check there is nothing wrong in there therefore the surprise factor is under control. This is an internal preview so the outcome is

• [ ] a GCS folder with the produced drug index

[JarrodBaker]

@d0choa: I have run the drug step with the Chembl28 inputs.

The outputs can be found here: gs://ot-team/jarrod/chembl-28-test

An overview of the outputs:

Counts: 

drug: 13076
drug_warnings: 1256
indication: 7427
mechanism_of_action: 5013

Columns for: drug
[
  "id",
  "canonicalSmiles",
  "inchiKey",
  "drugType",
  "blackBoxWarning",
  "name",
  "yearOfFirstApproval",
  "maximumClinicalTrialPhase",
  "parentId",
  "hasBeenWithdrawn",
  "isApproved",
  "withdrawnNotice",
  "tradeNames",
  "synonyms",
  "crossReferences",
  "childChemblIds",
  "count",
  "approvedIndications",
  "linkedTargets",
  "linkedDiseases",
  "description"
]

Columns for: drug_warnings
[
  "toxicityClass",
  "chemblIds",
  "country",
  "description",
  "id",
  "references",
  "warningType",
  "year",
  "meddraSocCode"
]

Columns for: indication
[
  "id",
  "indications",
  "count",
  "approvedIndications"
]

Columns for: mechanism_of_action
[
  "actionType",
  "mechanismOfAction",
  "chemblIds",
  "targetName",
  "targetType",
  "targets",
  "references"
]

At first glance the counts are correct (have actually increased from last run) and the columns look good. I haven't actually gone through the data manually, relying instead on the metadata output to get some summaries.

[andrewhercules]

Ticket closed as CHEMBL28 data has been ingested into the ETL pipelines and exposed by the GraphQL API (e.g. CHEMBL121 profile page shows the new warnings data introduced in CHEMBL28)