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monarch-initiative / phenopacket-store

Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.
https://monarch-initiative.github.io/phenopacket-store/
BSD 3-Clause "New" or "Revised" License
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Annotation inconsistencies #40

Closed ielis closed 10 months ago

ielis commented 10 months ago

@pnrobinson I ran C2S2 sanitizer to check for logical inconsistencies in annotations. I found some and I made a fix per commit. Can you pls check the diffs to see if the fixes look reasonable?

One weird thing in these phenopackets is that the HPO labels of the excluded features contain No in the text, e.g. No Abnormality of brain morphology, but the label should be Abnormality of brain morphology. Perhaps a quirk in pyphetools?

pnrobinson commented 10 months ago

@ielis Please do not change the phenopackets -- if we want this to happen then we need to change the code that is creating them. Let's talk today about the best way of doing this