RE: Provenence ontology in BioPortal

OK, I think that this is set up as agreed now. Please review it. The
Prov-o ontology has 30 classes and 50 properties. The Prov ontology (a
'view' on Prov-o) has 50 classes and 187 properties. 

 

Ray

 

From: Timothy Lebo [mailto:lebot@rpi.edu] 
Sent: Saturday, August 03, 2013 8:08 AM
To: Ray Fergerson
Cc: 'Helena Deus'; public-prov-comments@w3.org
Subject: 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> 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" <
<mailto:ray.fergerson@stanford.edu> 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@ <http://rpi.edu> rpi.edu] 
Sent: Wednesday, July 24, 2013 5:40 AM
To: Ray Fergerson
Cc: Helena Deus;  <mailto:public-prov-comments@w3.org>
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> 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>
http://lov.okfn.org/dataset/lov/details/vocabulary_prov.html

 

Regards,

Tim

 

[1]
<http://lists.w3.org/Archives/Public/public-prov-comments/2013Jun/0010.htm
l>
http://lists.w3.org/Archives/Public/public-prov-comments/2013Jun/0010.html

 

 

On Jul 23, 2013, at 5:52 PM, Ray Fergerson <
<mailto:ray.fergerson@stanford.edu> 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@ <http://stanford.edu> 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 < <mailto:lebot@rpi.edu>
lebot@rpi.edu> wrote:








Ray,

 

The Recommendation OWL can be found at  <http://www.w3.org/ns/prov>
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> 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 <
<mailto:ray.fergerson@stanford.edu> 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>
http://bioportal.bioontology.org/ontologies/3131/?p=summary

 

Below is a snippet from  your uploaded file.

 

Ray

 

 

<title>prov:
<mailto:ontology/ProvenanceOntology.owl@600c6fd1fdb4%3c/title>
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/> http://mercurial.selenic.com/"
title="Mercurial" style="float: right;">Mercurial</a>

<a href=" <http://dvcs.w3.org/hg/> 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 |