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enanomapper / slimmer

Slims ontologies.
https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-015-0005-5
MIT License
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Problem with NPO slim #18

Closed jannahastings closed 9 years ago

jannahastings commented 9 years ago

The latest version of the NPO slim file is not usable, as it generates an error in Protege / other OWL parsers. According to the error message from Protege, the problem is with an unknown prefix “ncicp” in the XML. This appears in the syntax used internally in the NPO for their definitions, e.g.

<npo:FULL_SYN rdf:datatype="http://www.w3.org/2001/XMLSchema#string">&lt;ncicp:ComplexTerm xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#&quot;&gt;&lt;ncicp:term-name&gt;cylindrical shape</ncicp:term-name><ncicp:term-group>PT</ncicp:term-group><ncicp:term-source>NCI</ncicp:term-source></ncicp:ComplexTerm>/npo:FULL_SYN

In previous versions of the slimmer, the output file produced for the NPO slim did not include the escaping of XML characters in the embedded definition, e.g. it used to include ncicp:ComplexDefinition whereas now it includes <ncicp:ComplexDefinition> This change must reflect an underlying change in the slimming software since nothing has changed in the underlying NPO OWL file.

jannahastings commented 9 years ago

@egonw This issue is kind of blocking me from adding content from NPO or updating the mappings of NPO to other classes. :-( I have been looking at this for a long time and I have NO IDEA what the problem is. Would be great if we could Skype about it some time.