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

Joanne Luciano jluciano at predmed.com
Fri Nov 17 17:34:44 PST 2006


Hi I think I needed to send this from a different email address.

To the list owner.... Please add my harvard address: jluciano at  
genetics.med.harvard.edu
Thanks.
Joanne


Begin forwarded message:

> From: protege-owl-owner at lists.stanford.edu
> Date: November 17, 2006 8:22:28 PM EST
> To: jluciano at genetics.med.harvard.edu
> Subject: BioPAX / SWOOP / Protege 4 Alpha / BioCyc / Missing  
> rdf:datatype property double in biopax.owl files from the biocyc  
> family
>
> You are not allowed to post to this mailing list, and your message has
> been automatically rejected.  If you think that your messages are
> being rejected in error, contact the mailing list owner at
> protege-owl-owner at lists.stanford.edu.
>
>
> From: Joanne Luciano <jluciano at genetics.med.harvard.edu>
> Date: November 17, 2006 8:22:08 PM EST
> To: Peter Karp <pkarp at AI.SRI.COM>, Biopax-Discuss <biopax- 
> discuss at cbio.mskcc.org>, User support for the Protege-OWL editor  
> <protege-owl at lists.Stanford.EDU>, swoop at lists.mindswap.org, p4- 
> feedback at lists.Stanford.EDU
> Subject: BioPAX / SWOOP / Protege 4 Alpha / BioCyc / Missing  
> rdf:datatype property double in biopax.owl files from the biocyc  
> family
>
>
> 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.
>
>
>
>



Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: jluciano at predmed.com



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