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Knowledge-Graph-Hub / kg-idg

A Knowledge Graph to Illuminate the Druggable Genome
https://knowledge-graph-hub.github.io/kg-idg/
BSD 3-Clause "New" or "Revised" License
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Add ATC information about drugs from Drug Central #42

Closed justaddcoffee closed 2 years ago

justaddcoffee commented 2 years ago

Describe the desired behavior

We'd like to ingest ATC level 1 information for drugs, which Jeremy Yang says in their SQL dump, in tables atc and struct2atc

Additional context

Per discussion with Tudor and Jeremy and others on the IDG call just now

caufieldjh commented 2 years ago

May be helpful to load in the full ATC set here too https://bioportal.bioontology.org/ontologies/ATC

caufieldjh commented 2 years ago

I don't see the tables 'atc' or 'struct2atc' in the TCRD SQL dump linked above. Perhaps they're in the DrugCentral dump: https://unmtid-shinyapps.net/download/drugcentral.dump.010_05_2021.sql.gz (but I haven't looked yet)

justaddcoffee commented 2 years ago

Yeah, possibly they are in the DrugCentral sql dump you linked.

Might be worth a moment to ping Jeremy to confirm we are getting what we think we are getting

caufieldjh commented 2 years ago

TCRD uses MySQL, so of course DrugCentral uses PostgreSQL. (A solvable issue.)