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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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Confirm a source for heritable phenotypic markers from OMIM #255

Closed kevinschaper closed 1 year ago

kevinschaper commented 2 years ago

I'm updating the OMIM ingest to remove nodes and make it edge-only. The gene nodes that it was previously making should all be taken care of SSSOM mapping to HGNC nodes, but we need to make sure that the we have nodes to map to for the NucleicAcidEntity nodes that it was making previously. We should be on the lookout for a big chunk of dangling OMIM edges after mapping. We may need to add a separate node ingest to bring these in with full node properties if OMIM is the right source for these nodes.

kevinschaper commented 1 year ago

It looks like there are about 1091 dangling edges from OMIM right now, but I think the alternative is that we would have edges connecting to NCBIGene IDs that themselves don't really connect to anything, so I'm just going to close this issue as being out of scope for the graph as we're building it right now.