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Orphanet / ORDO

Orphanet Rare Diseases Ontology
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Latest ORDO has some illegal chars (`<0xa0>`) in ICD11 mappings #37

Open matentzn opened 5 months ago

matentzn commented 5 months ago

Latest ORDO has some illegal chars (<0xa0>) in ICD11 mappings. They manifest at the latest part of the xref.

LC_ALL=C grep $'\u00A0' src/ontology/tmp/component-download-ordo.owl.owl 

LC_ALL=C grep $'\u00A0' src/ontology/tmp/component-download-ordo.owl.owl 
<oboInOwl:hasDbXref>ICD-11:1F70 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:1F70 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:7A20.0 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:7A20.0 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:FB82.1 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:FB82.1 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:4A43.Y </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:4A43.Y </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:FB82.1 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:FB82.1 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:2B5F.2 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:2B5F.2 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:LD24.1Y </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:LD24.1Y </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:2B57.1 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:2B57.1 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:EA50.2 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:EA50.2 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:4A60.1 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:4A60.1 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:2B33.2 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:2B33.2 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:2A80 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:2A80 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:4A01.12 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:4A01.12 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:1A36.00 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:1A36.00 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:JA65.0 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:JA65.0 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-10:N04.1 </oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>ICD-10:N04.3 </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-10:N04.1 </owl:annotatedTarget>
<owl:annotatedTarget>ICD-10:N04.3 </owl:annotatedTarget>
<oboInOwl:hasDbXref>ICD-11:LD24.A </oboInOwl:hasDbXref>
<owl:annotatedTarget>ICD-11:LD24.A </owl:annotatedTarget>
Orphanet commented 5 months ago

Thanks for the notification. Those non-breaking spaces seems to be part of the content in the database. Therefore they will be corrected soon. As the next ORDO release will be in june/july, we will probably will also make the modification directly into the OWL file before this next release.

davidlagorce commented 1 week ago

@matentzn We have corrected issues in Orphanet data that are employed to generate ORDO. In the next version (Jul 2024) soon available (maximum 2 weeks) you will not retreive such illegal chars. Best regards. David

matentzn commented 1 week ago

Thank you @davidlagorce!