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monarch-initiative / monarch-gene-mapping

Code for mapping source namespaces to preffered namespacing
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`{prefix}:<NA>` making it into output SSSOM #31

Closed kevinschaper closed 10 months ago

kevinschaper commented 1 year ago

It looks like something is up with the join to populate mappings and we're creating these weird mappings when an ID doesn't exist:

example:

HGNC:45103  skos:exactMatch OMIM:<NA>   semapv:UnspecifiedMatching
HGNC:34495  skos:exactMatch OMIM:<NA>   semapv:UnspecifiedMatching
HGNC:21224  skos:exactMatch OMIM:<NA>   semapv:UnspecifiedMatching

Unfortunately, there are 52k of them, spread out like this:

26730 HGNC -> OMIM
23417 HGNC -> UniProtKB
2692 HGNC -> ENSEMBL
  46 HGNC -> NCBIGene
kevinschaper commented 1 year ago

For our current stack, this isn't actually affecting anything since we look up IDs in the object column, and wouldn't look up <NA> (hopefully).

glass-ships commented 10 months ago

resolved in 0.1.5