Re: Provenence ontology in BioPortal

Ray,

On Aug 1, 2013, at 2:25 PM, "Ray Fergerson" <ray.fergerson@stanford.edu> wrote:

> Based on these responses, here is a suggestion:
>  
> We should load the provo.owl file as the main ontology for “Provenance Ontology” (PROVO)
> We can load the prov.owl file as a ‘view’ of the PROVO  ontology (even though it is a superset)

I'm not familiar with how BioPortal thinks about ontologies, but I agree that PROV-O is the "entry point" for developers to get started and PROV provides the kitchen sink.
Although it seems a bit backwards because "view" usually implies "subset", I'm willing to accept that inconsistency if it means that BioPortal users land on PROV-O before the dig in to get PROV.


>  
> We need a name for the superset ontology (view) in the prov.owl file. What  should this be called?

PROV is the superset of PROV-O

>  
> Also we need to know the location for the provo.owl file.
>  
> Prov:
> http://www.w3.org/ns/prov.owl
>  
> Provo:
> ???

http://www.w3.org/ns/prov-o.owl (the link mentioned in the abstract of the Recommendation http://www.w3.org/TR/prov-o) 


Once you make the changes, can you let me know so that I can see how it looks in BioPortal?

Thanks,
Tim



>  
> Ray
>  
> From: Timothy Lebo [mailto:lebot@rpi.edu] 
> Sent: Thursday, July 25, 2013 5:26 AM
> To: Ray Fergerson
> Cc: 'Helena Deus'; public-prov-comments@w3.org
> Subject: Re: Provenence ontology in BioPortal
>  
> Ray,
>  
> On Jul 24, 2013, at 6:32 PM, "Ray Fergerson" <ray.fergerson@stanford.edu> wrote:
> 
> 
> Timothy,
>  
> Since the file that I loaded is “prov.owl” can I assume that this is PROV and not PROV-O? Thus the acronym in BioPortal is currently wrong. Correct?
>  
>  
> That sounds reasonable.
>  
> 
> 
>  
> Based on your description, which I would paraphrase as: “Prov is the superset
>  
> Yes, PROV is the superset.
> 
> 
> that people will, in general want to use while PROV-O is a subset that some may find useful”,
>  
>  
> I would disagree with this. PROV-O is the subset that in general people will want to use. The rest of PROV is supplemental.
> This perspective is reflected by the fact that PROV-O is the Recommendation portion, and the rest has a lesser W3C publication status (Notes).
>  
> 
> 
> I would suggest making PROV the main ontology and PROV-O a BioPortal “View” of that ontology.
>  
> That sounds reasonable.
> 
> 
> Typically “Views” in BioPortal are ontologies that are logical subsets of other ontologies.
>  
> If this reasoning is all correct then I can probably massage things on our end to get the main ontology and view configured correctly.
>  
> I'll be happy to review your entries.
>  
> Best,
> Tim
> 
> 
>  
> Please confirm.
>  
> Ray
>  
> From: Timothy Lebo [mailto:lebot@rpi.edu] 
> Sent: Wednesday, July 24, 2013 5:40 AM
> To: Ray Fergerson
> Cc: Helena Deus; public-prov-comments@w3.org
> Subject: Re: Provenence ontology in BioPortal
>  
> Ray,
>  
> (cc'ing the prov comments list to archive the issue issue/resolution for accessing the OWL representation)
>  
> I don't see a `diff` between your new BioPortal copy and http://www.w3.org/ns/prov.owl, so it seems fine.
>  
>  
> A note on naming and ontology composition:
>  
> PROV is actually a union of several ontologies, one of which is PROV-O. PROV-O is the subset that fulfills the Recommendation, while PROV also includes the terminology for all other PROV-WG documents, including the DC-TERMS mapping, Access and Query, mentionOf/bundling linking, etc. This is described in metadata and provenance in the OWL file as RDF and as comments.
>  
> So, your catalog could choose to list both PROV and PROV-O, or pick one to list.
>  
> After some discussion on the W3C list [1], LOV recently chose to list the aggregate for PROV and none of its component ontologies http://lov.okfn.org/dataset/lov/details/vocabulary_prov.html
>  
> Regards,
> Tim
>  
> [1] http://lists.w3.org/Archives/Public/public-prov-comments/2013Jun/0010.html
>  
>  
> On Jul 23, 2013, at 5:52 PM, Ray Fergerson <ray.fergerson@stanford.edu> wrote:
> 
> 
> 
> Uploading the file directly seems to have produced something reasonable. Please have a look. It is quite possible that our download does not support content negotiation but it probably should.
>  
> Moving Trish to BCC on this message.
>  
> Ray
>  
> From: Trish Whetzel [mailto:whetzel@stanford.edu] 
> Sent: Tuesday, July 23, 2013 2:14 PM
> To: Timothy Lebo
> Cc: Ray Fergerson; Helena Deus
> Subject: Re: Provenence ontology in BioPortal
>  
> Hi Tim,
>  
> I was curating this, … Ray will be able to make updates to the metadata or assign admin privileges as requested.
>  
> Trish 
>  
>  
> On Jul 23, 2013, at 1:06 PM, Timothy Lebo <lebot@rpi.edu> wrote:
> 
> 
> 
> 
> Ray,
>  
> The Recommendation OWL can be found at http://www.w3.org/ns/prov
>  
> As that page states, the OWL representation of the ontology can be obtained as Turtle or RDF/XML using content negotiation.
>  
> If you can't use content negotiation, you can access the OWL directly using http://www.w3.org/ns/prov.owl
>  
>  
>  
> @Trish, I'm cc'ing you b/c you've asked about PROV-O and you seem to have been curating the BioPortal entry.
> I don't have access to edit BioPortal and am not planning to use it. Who can update this entry?
>  
>  
>  
> @Helena, your name came up to, can you update the entry to something that BioPortal'ers find useful?
>  
>  
> Thanks,
> Tim
>  
>  
>  
>  
>  
> On Jul 19, 2013, at 4:55 PM, Ray Fergerson <ray.fergerson@stanford.edu> wrote:
> 
> 
> 
> 
> Tim,
>  
> The file uploaded for this ontology is just an html page. It is not an OWL file. Can you upload a real ontology? Do you want us to delete it instead?
>  
> http://bioportal.bioontology.org/ontologies/3131/?p=summary
>  
> Below is a snippet from  your uploaded file.
>  
> Ray
>  
>  
> <title>prov: ontology/ProvenanceOntology.owl@600c6fd1fdb4</title>
> <link rel="alternate" type="application/atom+xml"
>    href="/hg/prov/atom-log" title="Atom feed for prov"/>
> <link rel="alternate" type="application/rss+xml"
>    href="/hg/prov/rss-log" title="RSS feed for prov"/>
> </head>
> <body>
>  
> <div class="page_header">
> <a href="http://mercurial.selenic.com/" title="Mercurial" style="float: right;">Mercurial</a>
> <a href="http://dvcs.w3.org/hg/" >Home</a> /
> <a href="/hg/prov/summary">prov</a> / file revision
> </div>
>  
> <div class="page_nav">
> <a href="/hg/prov/summary">summary</a> |
> <a href="/hg/prov/shortlog">shortlog</a> |
> <a href="/hg/prov/log">changelog</a> |
> <a href="/hg/prov/graph">graph</a> |
> <a href="/hg/prov/tags">tags</a> |
> <a href="/hg/prov/branches">branches</a> |
> <a href="/hg/prov/file/600c6fd1fdb4/ontology/">files</a> |
> <a href="/hg/prov/rev/600c6fd1fdb4">changeset</a> |
> file |
>