strange occurrence of rdf:nodeID

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strange occurrence of rdf:nodeID

damion

 I’m hoping someone has seen this before and knows exactly the answer in 5 seconds.  The issue started this morning, when I saved the foodon-edit.owl file in protégé.  The resulting diff was weird  It began with removal of every line of existing file, and insertion of all new file, even though they began with same content line by line.  Both versions display the same in protégé .  Further down the files differ significantly.  Normally it has a lot of owl:Class:

 

     <!-- http://purl.obolibrary.org/obo/FOODON_03412142 -->

 

    <owl:Class rdf:about="&obo;FOODON_03412142">

        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>

        <obo:IAO_0000412>http://langual.org</obo:IAO_0000412>

        <obo:IAO_0100001 rdf:resource="&obo;FOODON_03413891"/>

        <rdfs:label xml:lang="en">obsolete argentine hake</rdfs:label>

        <owl:deprecated rdf:datatype="&xsd;boolean">true</owl:deprecated>

    </owl:Class>

 

But ALL just got changed to <rdf:Description>:

 

<!-- http://purl.obolibrary.org/obo/FOODON_03412142 -->

 

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/FOODON_03412142">

                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>

                <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>

                <obo:IAO_0000412>http://langual.org</obo:IAO_0000412>

                <obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/FOODON_03413891"/>

                <rdfs:label xml:lang="en">obsolete argentine hake</rdfs:label>

                <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>

</rdf:Description>

 

Which would be bearable but I think rdf:Description is causing lots more anonymous nodes from rdf list, thousands. I’m now getting stuff like:

 

<rdf:Description rdf:nodeID="genid4578">

                <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#List"/>

                <rdf:first rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001474"/>

                <rdf:rest rdf:nodeID="genid4577"/>

</rdf:Description>

 

<rdf:Description rdf:nodeID="genid4577">

                <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#List"/>

                <rdf:first rdf:resource="http://purl.obolibrary.org/obo/UBERON_0006611"/>

                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>

</rdf:Description>

 

And those genid4578 etc. are INCREMENTING on each GitHub edit/save/push no matter how small the edit on the file.

Anybody seen this, and how to avert it?  I’ve tried running a “robot reduce” command after the fact, which does convert the protege saved content back into predominantly classes, and no anonymous ids.  But I don’t want to have to foist that step onto our other curators.


Help appreciated.  Using java 11 2018-09-25, and protege 5.5.0

Regards,

Damion

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Re: strange occurrence of rdf:nodeID

Balhoff, James Patrick
Hi Damion,

Sorry this doesn’t really answer your question (I don’t know what is triggering the different RDF/XML representations), but I just want to say I really like OWL Functional syntax for the version-controlled file. The file will have a single line per axiom, resulting in clean diffs on GitHub. Example:


You can always output to an RDF format for your released ontology.

- Jim


On May 8, 2020, at 10:21 PM, Damion Dooley <[hidden email]> wrote:

 I’m hoping someone has seen this before and knows exactly the answer in 5 seconds.  The issue started this morning, when I saved the foodon-edit.owl file in protégé.  The resulting diff was weird  It began with removal of every line of existing file, and insertion of all new file, even though they began with same content line by line.  Both versions display the same in protégé .  Further down the files differ significantly.  Normally it has a lot of owl:Class:

 

     <!-- http://purl.obolibrary.org/obo/FOODON_03412142 -->

 

    <owl:Class rdf:about="&obo;FOODON_03412142">

        <rdfs:subClassOf rdf:resource="&oboInOwl;ObsoleteClass"/>

        <obo:IAO_0000412>http://langual.org</obo:IAO_0000412>

        <obo:IAO_0100001 rdf:resource="&obo;FOODON_03413891"/>

        <rdfs:label xml:lang="en">obsolete argentine hake</rdfs:label>

        <owl:deprecated rdf:datatype="&xsd;boolean">true</owl:deprecated>

    </owl:Class>

 

But ALL just got changed to <rdf:Description>:

 

<!-- http://purl.obolibrary.org/obo/FOODON_03412142 -->

 

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/FOODON_03412142">

                <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>

                <rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>

                <obo:IAO_0000412>http://langual.org</obo:IAO_0000412>

                <obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/FOODON_03413891"/>

                <rdfs:label xml:lang="en">obsolete argentine hake</rdfs:label>

                <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>

</rdf:Description>

 

Which would be bearable but I think rdf:Description is causing lots more anonymous nodes from rdf list, thousands. I’m now getting stuff like:

 

<rdf:Description rdf:nodeID="genid4578">

                <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#List"/>

                <rdf:first rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001474"/>

                <rdf:rest rdf:nodeID="genid4577"/>

</rdf:Description>

 

<rdf:Description rdf:nodeID="genid4577">

                <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#List"/>

                <rdf:first rdf:resource="http://purl.obolibrary.org/obo/UBERON_0006611"/>

                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>

</rdf:Description>

 

And those genid4578 etc. are INCREMENTING on each GitHub edit/save/push no matter how small the edit on the file.

Anybody seen this, and how to avert it?  I’ve tried running a “robot reduce” command after the fact, which does convert the protege saved content back into predominantly classes, and no anonymous ids.  But I don’t want to have to foist that step onto our other curators.


Help appreciated.  Using java 11 2018-09-25, and protege 5.5.0

Regards,

Damion
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user