search

monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
14 stars 1 forks source link

Drug Central Ingest #457

Open putmantime opened 1 year ago

putmantime commented 1 year ago

We will extract associations from DrugCentral including “Indication”, “ContraIndication”, “Adverse Event” and “Off-Label Use” relationships between drugs and diseases.

We need to extract the required data from DrugCentral’s Postgres Database. Drug entities in DrugCentral have a variety of identifiers, such as from RxNorm, CAS, InChIKey, etc.

We will need to collaborate with DrugCentral to decide on faceting, thresholds and query design.

justaddcoffee commented 1 year ago

nb: @caufieldjh wrote some code to extract stuff from drug central's sql dumps for KG-IDG, see here

caufieldjh commented 1 year ago

ah, @justaddcoffee got there first, I was just about to post that

Would be happy to chat about DrugCentral specifics

monicacecilia commented 5 months ago

Dear @justaddcoffee @caufieldjh @kevinschaper, was there a conversation about this? Was it resolved?

caufieldjh commented 5 months ago

This was not resolved. It's worth noting that the obo-db-ingest project also has some pre-transformed DrugCentral serializations - https://github.com/biopragmatics/obo-db-ingest/tree/main/export/drugcentral These don't cover as much detail as the current KG-IDG ingest (e.g., KG-IDG includes details like FDA approval status). So some decision on use case would be helpful here.