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[p4-feedback] BioPAX / SWOOP / Protege 4 Alpha / BioCyc / Missing rdf:datatype property double in biopax.owl files from the biocyc family

Joanne Luciano jluciano at genetics.med.harvard.edu
Fri Nov 17 17:22:08 PST 2006


FYI:

In the current biocyc family of biopax.owl files, the following  
property statements will cause "inconsistent" ontologies in SWOOP and  
Protege4Alpha.

<bp:MOLECULAR-WEIGHT>18.015</bp:MOLECULAR-WEIGHT>
<bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
<bp:DELTA-G>0.4    </bp:DELTA-G>

In SWOOP this error message will read:
> Consistent: No
> Reason: Plain literal "18.015" does not belong to datatype http:// 
> www.w3.org/2001/XMLSchema#double. Literal value may be missing the  
> rdf:datatype attribute.

In Protege4Alpha an error message indicates that the ontology is  
inconsistent, but no message yet as to why.  However in the  
individuals tab, the Value associated with the Property (MOLECULAR- 
WEIGHT or STOICHIOMETRIC-COEFFICIENT or DELTA-G) indicates the error.  
For example:

Property									Value
bpx1:MOLECULAR-WEIGHT 				<Error! null>


To fix these, you can globally add the rdf:datatype property so the  
statements look like this:
<bp:MOLECULAR-WEIGHT rdf:datatype="http://www.w3.org/2001/ 
XMLSchema#double">186.058</bp:MOLECULAR-WEIGHT>
<bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/ 
XMLSchema#double">1</bp:STOICHIOMETRIC-COEFFICIENT>
<bp:DELTA-G rdf:datatype="http://www.w3.org/2001/ 
XMLSchema#double">0.4    </bp:DELTA-G>

I did a global search and replace of
this														with this
<bp:MOLECULAR-WEIGHT>								<bp:MOLECULAR-WEIGHT  
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
<bp:STOICHIOMETRIC-COEFFICIENT>					<bp:STOICHIOMETRIC-COEFFICIENT  
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
<bp:DELTA-G>											<bp:DELTA-G rdf:datatype="http://www.w3.org/ 
2001/XMLSchema#double">

Thanks to Bijan Parsia for help in tracking this down.





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