phenopackets/phenopacket-tools

pseudoexfoliation.json has both SNOMEDCT and SCTID namespaces

cmungall opened this issue · 2 comments

cmungall commented 
      "id": "SCTID:414775001",
      "id": "SCTID:397312009",
      "id": "SCTID:397312009",

      "id": "SNOMEDCT:252886007",

It's best to use consistent prefixes. I recommend bioregistry to determine which is canonical:

https://bioregistry.io/registry/snomedct

cmungall commented

linkml-phenopackets has a command line tool that will detect bad CURIEs and fix them using bioregistry:

 p3 normalize-curies examples/Phenopacket-pseudoexfoliation.yaml
p3 normalize-curies examples/Phenopacket-pseudoexfoliation.yaml -o /tmp/Phenopacket-pseudoexfoliation-fixed.yaml
## Num results: 3
## RESULT: ('SCTID:397312009', 'SNOMEDCT:397312009')
## RESULT: ('SCTID:397312009', 'SNOMEDCT:397312009')
## RESULT: ('SCTID:414775001', 'SNOMEDCT:414775001')
ielis commented

Hi @cmungall thanks a lot for pointing out this issue. I fixed the invalid prefixes and the validation now works OK.