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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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Generate SSSOM for drug CURIEs to DrugCentral #71

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Addressing #46

This includes a curated map in the maps directory - ideally this would be generated automatically as part of the DrugCentral transform using the identifier DB table, as this is sufficient to map CURIEs. This lacks the names of external CURIEs, however, and many of these are non-trivial to retrieve (e.g., PubChem compound IDs) unless we only do it for updates rather than full sets of IDs. For this reason, the curated map can start as the basic foundation for drug ID maps in this project or others.

This PR also includes some improvements to DrugCentral identifier transform parsing, retrieves drug names while parsing drug-target interactions, and ensures proteins are assigned category (just in case they don't get assigned it by ingests other than TCRD's protein table).

sonarcloud[bot] commented 2 years ago

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
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