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monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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Reactome pathway node ingest #186

Closed kevinschaper closed 2 years ago

kevinschaper commented 2 years ago

We have two association/edge ingests for Reactome, but we don't have a node ingest for bringing in pathways with the name (and maybe taxon?).

https://reactome.org/download/current/ReactomePathways.txt

Columns:

Looking at Biolink model, I don't see in_taxon as a property of Pathways, so that's the one part of this that I'm not sure how to handle.

putmantime commented 2 years ago

Species may not be an option in Biolink pathway.

putmantime commented 2 years ago

Reopenning because I see in the kgx nodes file reactome_pathway_nodes.tsv that there is no 'category' column.