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Looking at getSpontaneous() in .owl files. Confusion ensues.

asked 2016-11-16 17:03:32 -0600

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Hello,

I'm parsing the L3 .owl files generated by pathway-tools using paxtools and have run into something confusing. I'm trying to determine which reactions are spontaneous.

The paxtools call to determine this is Conversion.getSpontaneous() from what I can tell. When I call this function on BiochemicalReactions in an .owl file, I get null most of the time (meaning that it is undetermined), and 'false' for all other times it is not null. From what I can tell, the reactions in which the value is false have lines in the .owl file:

   <bp:spontaneous rdf:datatype="http://www.w3.org/2001/XMLSchema#string">L-R</bp:spontaneous>

that would seem to me to say getSpontaneous() should return true.

FWIW, in the owl file distributed with Paxtools (biopax3-short-metabolic-pathway.owl), there is a corresponding line:

This appears to be true in pathway-tools files written with either v19 or v20. And with paxtools 4.3.1 and 5.0.0-20160601 <bp:spontaneous rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</bp:spontaneous>

Is there a problem with pathway-tools writing the string instead of a boolean, or with paxtools not parsing a string value?

Thanks,

Joe Carlson

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Sorry. Some of the lines got mixed up. Here is the corrected FWIW, in the owl file distributed with Paxtools (biopax3-short-metabolic-pathway.owl), there is a corresponding line: <bp:spontaneous rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</bp:spontaneous>

JW Carlson gravatar imageJW Carlson ( 2016-11-16 17:11:35 -0600 )edit

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answered 2016-12-19 16:35:41 -0600

Suzanne Paley gravatar image

A patch for this problem is now available (v.20.0 and later only).

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Asked: 2016-11-16 17:03:32 -0600

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Last updated: Dec 19 '16