Re: Using PROV-O to represent ontology processing, extraction and reasoning operations

Chris,
  seems very reasonable to use prov:wasGenerated By <activity>. feel free
to explicitly add "a prov:Activity" to your foo/op1.

m.

On Sat, Nov 25, 2017 at 7:46 PM, Chris Mungall <cjmungall@lbl.gov> wrote:

> I had anticipated using prov:wasAssociatedWith, and not creating any new
> properties. The gap to be filled is on the side of subclasses of
> prov:Activity, for representing operations specific to ontology processing.
>
> Assuming such an ontology, does this rough sketch seem like a standard
> pattern? Is there a good analogous set of design patterns to follow (e.g.
> software compilation, scientific workflows)?
>
> @prefix prov: <http://www.w3.org/ns/prov#> .
> @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
> @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix owl: <http://www.w3.org/2002/07/owl#> .
> @prefix obo: <http://purl.obolibrary.org/obo/> .
> @prefix opera: <http://example.org/OntologyProcessingExtractionReasoningOntology/> .
>
> ## Ontology header
> obo:foo.owl a owl:Ontology ;
>    dc:title "..." ;
>    prov:wasDerivedFrom obo:foo/foo-edit.owl ;
>    prov:wasGeneratedBy obo:foo/op1 ;    ## see below
>    prov:wasAttributedTo obo:foo/editors ;
>    ...
>
> ## Ontology provenance
> obo:foo/op1 a opera:ReasonOperation ;
>    prov:used obo:foo/foo-edit.owl ;     ## 'source code'
>    prov:wasInformedBy <configuration??> ## what to use here?
>    prov:startedAtTime "..." ;
>    prov:endedAtTime "..." ;
>    prov:wasAssociatedWith <github/mavenOrGithubIRIforROBOTversion??> ;
>
> ## Ontology below
> obo:FOO_0000001 a owl:Class ;
>     ...
>
> On 25 Nov 2017, at 0:29, Graham Klyne wrote:
>
> Is there any reason that http://www.w3.org/TR/prov-o/#wasAssociatedWith
> doesn't work for you?
>
> My recollection of PROV discussions is that involvement of human, software
> and other agents in an activity was intended to be captured using this (or
> qualifiedAssociation structures - cf. http://www.w3.org/TR/prov-o/#
> qualifiedAssociation).
>
> (IIRC, the "qualifiedAssociation" and similar structures --
> http://www.w3.org/TR/prov-o/#description-qualified-terms -- were
> introduced to avoid application-dependent (not a priori defined)
> sub-properties, which would break OWL-QL compatibility of PROV, with
> attendant reasoning performance challenges.)
>
> #g
> --
>
> On 24/11/2017 22:15, Chris Mungall wrote:
>
> Many ontologies such as those in the life-sciences have complex multi-step
> release pipelines: for example, using an OWL reasoner to assert direct
> inferred
> subClassOf axioms, adding owl annotations, verifying using SPARQL. It
> would be
> useful to capture the full operation graph, so that the provenance of the
> released ontology was explicit.
>
> PROV-O would provide the main framework for doing this. PROV-O predicates
> could
> be used directly. Existing standards could be used to represent the
> software
> agents involved. AFAICT there is a gap for an ontology for representing the
> ontology processing operations (subclasses of prov:Activity).
>
> Is there an existing effort that could be piggy-backed on here? This could
> be
> subsumed into an effort that seeks to represent for example transformations
> between named graphs. Alternatively, the ontology build pipeline could be
> conceived either as a software release process or a scientific workflow.
> For the
> latter, there are a number of ontologies but it's not clear we'd get any
> benefit
> using these rather than PROV-O directly.
>
> If there is no existing work being done here, I'll propose a draft of
> activity
> classes and design patterns, and we can do a demo implementation in our
> ontology
> release tool [ROBOT](https://github.com/ontodev/robot). But I'd rather not
> duplicate any existing efforts.
>
>


-- 
Michel Dumontier
Distinguished Professor of Data Science
Maastricht University
http://dumontierlab.com