Re: [Prov-O] Review of examples

Stian,

Thanks for working through this.
It's clear that it needs to be done, with all of the errors that you're finding :-)

As we agreed in the call yesterday, these last details are needed as we push towards final Rec, so let's carry the ball bit by bit over the coming weeks.

Regards,
Tim

On Jul 3, 2012, at 7:18 AM, Stian Soiland-Reyes wrote:

> This email is mainly my notes as I have been checking the examples
> used by PROV-O to make sure they are valid RDF and valid according to
> the ontology.
> 
> I would need volunteers to complete the job (such as fixing the
> examples that are broken!). Any takers? Also suggestions on other ways
> to check this would be appreciated.
> 
> 
> 
> I've made a little shell script that checks all PROV-O examples (which
> again are embedded into HTML):
> 
> http://dvcs.w3.org/hg/prov/file/fd4982cfd7f7/examples/eg-24-prov-o-html-examples/rdf/create/check-examples.bash
> 
> It uses CWM to check the syntax only, assuming N3 rather than Turtle.
> The output is the filename if it is OK, or error message on stderr:
> 
> 
>> stain@ralph-ubuntu:~/src/prov/examples/eg-24-prov-o-html-examples/rdf/create$ ./check-examples.bash
>> rdf/property_qualifiedDerivation.ttl
>> rdf/property_inserted.ttl
>> 
>> (..)
>>    Failed to parse file:///home/stain/src/prov/examples/eg-24-prov-o-html-examples/rdf/create/rdf/class_ContextualizedEntity.ttl
>>   file:///home/stain/src/prov/examples/eg-24-prov-o-html-examples/rdf/create/rdf/class_ContextualizedEntity.ttl
>> Traceback (most recent call last):
>>  File "/usr/local/bin/cwm", line 750, in <module>
>>    doCommand()
>> rdf/property_hasAnchor.ttl
>> rdf/property_key.ttl
>> (..)
>> stain@ralph-ubuntu:~/src/prov/examples/eg-24-prov-o-html-examples/rdf/create$
> 
> 
> Some of these errors are due to them being in TriG format rather than
> Turtle format, which is not supported by CWM.
> 
> The remaining syntax errors I have corrected and committed.
> 
> 
> If we use this style for the named graphs:
> 
> :G1 = {
>  :a :b :c
> } .
> 
> Then it is valid N3 (but not Turtle), and can be included in the test.
> I changed this temporarily (not checked in) using:
> 
> for f in $(find rdf -name '*ttl') ; do cat $f | sed 's/{$/= {/' | sed
> 's/^}/} ./' > /tmp/$$ && cp /tmp/$$ $f ; done
> 
> .. to ensure they are valid enough - and then check with
> ./check-examples.bash again.
> 
> 
> BTW - I found it odd that prov:Note is asserted inside the note graph
> in rdf/class_Note.ttl and rdf/class_Trace.ttl, rather than in the
> graph outside that has prov:hasAnnotation - so I moved that out. (Also
> I guess we don't want to reinvent an annotation ontology -
> http://www.w3.org/community/openannotation/ )
> 
> 
> 
> Then on to checking if there are some spelling wrong, like prov:Acvititity.
> 
> To include the named graph files in this, I temporarily flattened them
> rather than use the Turtle syntax:
>  hg revert -C rdf
>  for f in $(find rdf -name '*ttl') ; do cat $f | sed 's/{$/ a
> prov:Entity ./' | sed 's/^}//' > /tmp/$$ && cp /tmp/$$ $f ; done
>  hg revert -C rdf
> 
> 
> 
> 
> I've made a little shell script that merges all the PROV-O examples to
> a single TTL file - ./merge-examples.bash
> 
> This generates merged.ttl - see
> http://dvcs.w3.org/hg/prov/file/tip/examples/eg-24-prov-o-html-examples/rdf/create/merged.ttl
> 
> (Note - you do not need to do the above sed-trick if you are OK to
> ignore the 4-5 TriG files from the merge - merge-examples will
> silently skip files that don't parse)
> 
> 
> 
> 
> I then opened merged.ttl in Protege 4.2 beta, and saved it out again in Turtle:
> 
> http://dvcs.w3.org/hg/prov/file/a068151bca91/examples/eg-24-prov-o-html-examples/rdf/create/implied.owl
> 
> 
> As a side note - to distinguish between 'our' classes (like Painting)
> and classes in other namespaces, like prov:Activity - turn on prefix
> qnames by going to View -> Custom rendering -> Render by Qualified
> Name.
> 
> 
> 
> As you see, Protege has filled in the blanks for 'new' classes and
> properties, such as:
> 
> prov:inContext rdf:type owl:AnnotationProperty .
> prov:contextualized rdf:type owl:AnnotationProperty .
> prov:hadQuoter rdf:type owl:AnnotationProperty .
> (..)
> prov:Actvity rdf:type owl:Class .
> prov:CompleteCollection rdf:type owl:Class .
> 
> 
> 
> 
> Now, the boring job (which I have not done - any takers?) - is to go
> through this list for the properties and classes (you can ignore
> 'Individuals') - and for any prov: keyword, look in merged.ttl to see
> where it came from.
> 
> For instance, prov:hadQuoter - can be found in merged.ttl as:
> 
> @base <http://dvcs.w3.org/hg/prov/raw-file/tip/examples/eg-24-prov-o-html-examples/rdf/create/rdf/property_hadQuoter.ttl>
> .
> # ...
>      prov:hadQuoter <http://data.semanticweb.org/person/luc-moreau>;
> # ...
> 
> And so it is rdf/property_hadQuoter.ttl that needs to be fixed (or deleted).
> 
> 
> 
> The final step is in Protege 4.2 is to turn on the Reasoner and see if
> our mega-merge is consistent. This turn out not to be the case - but
> mainly because we have reused some terms in the examples - like :
> 
> * First flip in the top drop-down box to PROV-O to run the reasoner on this.
> * Under Reasoner, select Fact++
> * Under Reasoner, click Start Reasoning
> ** This should succeed
> * Now in the drop-down, go back to merged.ttl
> * Under Reasoner, click Start Reasoning
> ** It will complain that the ontology is inconsistent
> ** Wait 2 seconds (not sure why)
> ** Click "Explain"
> *** Protege will compute explanations for a while, I got at least 36
> before I clicked Stop.
> 
> Unfortunately I don't seem to be able to export the explanations in text form.
> 
> 
> Example explanation:
> 
>> 'The Painter' invalidatedAtTime "2012-09-02T01:31:00Z"
>> invalidatedAtTime Range: dateTime
> 
> (here the error is probably that ^^xsd:dateTime is missing in the literal)
> 
> 
>> filling-fuel endedAtTime "2012-04-24T18:31:00Z"^^xsd:dateTime
>> Functional: startedAtTime
>> filling-fuel endedAtTime "2012-04-24T18:21:00Z"^^xsd:dateTime
> 
> (Here the error is that two examples state endedAtTime for the same
> instance - but have different literal values)
> 
> 
>>> draft2 qualifiedAssociation _:genid113
>> Activity DisjointWith Entity
>> qualifiedAssociation Domain Activity
>> draft2 wasRevisionOf e1
>> wasRevisionOf Domain Entity
> 
> Here the problem is that 'draft2' has been asserted with both
> wasRevisionOf and qualifiedAssociation - but their domains are
> disjoint; it can't both be an Activity and Entity. This bug is in
> rdf/class_Revision.ttl.
> 
> 
> There are a few more - but there are some common patterns. I suggest:
> 
> * Rename example instances that are distinct
> * Fix errors such as qualifiedAssociation above (check: Is the error
> in the example or the OWL? Note that merged.ttl imports from
> http://dvcs.w3.org - so if you change ProvenanceOntology.owl - do a
> push before reloading in Protege)
> * Re-merge and try again ..
> 
> 
> 
> Once the ontology is consistent - it is possible to do File -> Export
> inferred axioms to ontology.
> 
> As an exercise - here are the inferred axioms from ProvenanceOntology.owl:
> 
> http://dvcs.w3.org/hg/prov/file/a068151bca91/examples/eg-24-prov-o-html-examples/rdf/create/implied-provo.owl
> 
> I've had a look at this, and most of this are obvious inferences that
> reasons need:
> 
>    56 <http://www.w3.org/ns/prov#agent> rdf:type owl:ObjectProperty ;
>    60                                   owl:inverseOf [ owl:inverseOf
> <http://www.w3.org/ns/prov#agent>
>    61                                                 ] .
> 
> (this could be one of the reasons why we don't have inverses for every
> property!)
> 
> I looked through this list and did not find anything controversial.
> 
> 
> 
> 
> -- 
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
> 
>

Received on Tuesday, 3 July 2012 12:21:26 UTC