Metadata on CarveMe run process/version wrongly added to model #219
Description
Handling the metadata information for the desciption of the building process is handled strangely in the newest version of CarveMe. Backtracking this problem lead me to reframed. Further details on the problem are given below:
While CarveMe version 1.5.1, with the reframed version 1.2.1, added the metadata from the CarveMe runs like this:
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<p>Description: This model was built with CarveMe version 1.5.1</p>
<p>This is a metabolism model of ${organism} in
<a href="http: //sbml.org" target="_blank" title="Access the definition of the SBML file format.">SBML</a> format.</p>
<p>Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met: <ol>
<li>Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.</li>
<li>Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.</li>
</ol>This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</p>
<p>For specific licensing terms about this particular model and regulations of commercial use, see
<a href="http: //identifiers.org/bigg.model/${bigg_id}" title="Access to this model via BiGG Models knowledge-base." target="_blank">this model in BiGG Models knowledge-base</a>.</p>
</html>
</notes>The newest version adds the metadata like this:
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_iShaJCSC1435GOD25">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="https://identifiers.org/Description/This model was built with CarveMe version 1.6.4"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>This is an incorrect annotation string with an invalid URI, and the relationship also does not fit.
Offering an annotation for the model with the relation BQM_IS_INSTANCE_OF or BQM_HAS_INSTANCE and a valid URI for the CarveMe universe model or a user-specified model would be nice metadata information to include. Otherwise, it would be better to use the old version, where the description of the building process remained in a notes field for the model object.