Re: [Prov-O] Review of examples

Tracker, this is 

ISSUE-349

-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 Thursday, 5 July 2012 16:43:55 UTC