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BioPAX contains invalid RDF/XML #36

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cmungall opened this issue Oct 20, 2022 · 0 comments
Open

BioPAX contains invalid RDF/XML #36

cmungall opened this issue Oct 20, 2022 · 0 comments

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@cmungall
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reporting on behalf of @vdancik

From INCATools/semantic-sql#59

http://data.pantherdb.org/ftp/pathway/current_release/BioPAX.tar.gz contains invalid RDF/XML, Rust RDF parsers will throw an error

It looks like the OWL is not valid RDF/XML. Rust uses a stricter parser than the OWLAPI or Jena, so these kinds of problems slip by...

The problem is here:

<bp:UnificationXref rdf:ID="eco_ECO:0000501_12">
 <bp:id rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">ECO:0000501</bp:id>
 <bp:db rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">eco</bp:db>
</bp:UnificationXref>

this is invalid RDF and eco_ECO is not defined

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