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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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Convert Reactome Gene to Pathway to use NCBI2Reactome #266

Closed kevinschaper closed 2 years ago

kevinschaper commented 2 years ago

It looks like we can save ourselves a lot of mapping trouble by switching from Ensembl2Reactome.txt to NCBI2Reactome.txt, and we should also filter the species list down to match our species list.

We'll need to change out the url for https://reactome.org/download/current/NCBI2Reactome.txt and change the prefix added to NCBIGene

There are also a few non-integer entries in the component column that we either need to filter out or handle differently. 

MN908947.3
NC_004718.3
NM_000077.4
NM_001244810
NM_058195.3
NR_006880
NR_046235
U13369

The alternative to this would involve things like making mapping files from yeast systematic names to SGD IDs.

RichardBruskiewich commented 2 years ago

Blocked awaiting a fresh Biolink Model release with PR's 1031 and 1033, which revised the model to accommodate elements which I used in the code PR for this issue.

sagehrke commented 2 years ago

@kevinschaper please review.