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Re: Workflow Example in Formal Model HTML document

From: Satya Sahoo <satya.sahoo@case.edu>
Date: Fri, 30 Sep 2011 20:11:53 -0400
Message-ID: <CAOMwk6zZY6MMn1=yZaEoCwmvwxh8Rk_oc3Bv=V5yZuG3cy0x8g@mail.gmail.com>
To: James Cheney <jcheney@inf.ed.ac.uk>
Cc: Luc Moreau <L.Moreau@ecs.soton.ac.uk>, Khalid Belhajjame <Khalid.Belhajjame@cs.man.ac.uk>, Stian Soiland-Reyes <soiland-reyes@cs.manchester.ac.uk>, Daniel Garijo <dgarijov@gmail.com>, Timothy Lebo <lebot@rpi.edu>, "Deborah L. McGuinness" <dlm@cs.rpi.edu>, Paolo Missier <pmissier@acm.org>, Provenance Working Group WG <public-prov-wg@w3.org>
Hi James,
I am afraid we are mixing up multiple issues here.

>entities are intended to denote "things in the world", while provenance
containers (and accounts) are syntactic things that >don't necessarily
denote real-world things

Every resource/thing in any computer-based information system is a
representative/placeholder of some thing in a "domain of discourse". I am
not sure what metric you are using to define a "thing in the world".

To understand your point better, can you please identify "thing in the
world" among the following examples:
1. "particular execution of a scientific workflow"

2. "a text file on a computer hard drive" (not its print out on paper, that
is a distinct thing)

3. "a signaling pathway in mouse brain" (signaling pathway is a special type
of biological pathway, which is defined as "A *biological pathway* is a
series of actions among molecules in a cell that leads to a certain product
or a change in a cell." from www.genome.gov - in other words there is no
concrete structure that we can touch and say it is a biological pathway)

4. "idea, which is patented, to increase efficiency of petrol-based internal
combustion engine"

In provenance applications, we make provenance assertions about each of the
above four things. Further, almost all of them are used to organize data
(information) as an abstraction mechanism.

>By analogy, in mathematics we can talk about "the set of all people whose
first initial is Z" without there necessarily being >a real-world thing
corresponding to this set.

In Web application (the scope for our WG work) - we are dealing with
representation of "people" and not real persons. Hence, both terms "people"
and "set of people with initial Z" are syntactic constructs we define to
work with and then define rules for their interpretation that associates
semantics with the constructs.

My understanding of both Entity and Provenance Container are in line with
the above points, that is, both are syntactic constructs. Both can be used
represent things in our domain of discourse.

> I think we need to distinguish between syntax and semantics carefully
Exactly, hence I will wait for your mail in response to my above points and
then I will comment on the rest of your mail.



On Thu, Sep 29, 2011 at 5:15 AM, James Cheney <jcheney@inf.ed.ac.uk> wrote:

> Hi Satya,
> I missed the beginning and end of the teleconference Monday, but I wanted
> to say that my interpretation of provenance containers (and accounts etc.,
> which seem related) has been that entities are intended to denote "things in
> the world", while provenance containers (and accounts) are syntactic things
> that don't necessarily denote real-world things, need not be changeable over
> time, but instead are used in the syntax of the model to organize data.  By
> analogy, in mathematics we can talk about "the set of all people whose first
> initial is Z" without there necessarily being a real-world thing
> corresponding to this set.
> I haven't tried making this explicit in the formal semantics yet since I
> wanted to get the basic stuff right first.
> One could certainly (if one wanted to) *introduce* an entity that stands
> for a particular provenance container, say a physical envelope that contains
> pieces of paper with provenance assertions written on them, and use
> annotations (or some other way) to relate the entity with the container and
> relate  the pieces of paper to other entities and to their corresponding
> data model instances.  Or, one could introduce a subclass of Entity called
> ContainerEntity, that represents real-world things that can contain things
> (including things that carry provenance information).  This would be a
> separate concept from how I understood ProvenanceContainer.
> Your suggestion that any ProvenanceContainer is an Entity seems to me to
> impose an unnecessary level of meta-ness - I think we need to distinguish
> between syntax and semantics carefully here.
> --James
> On Sep 29, 2011, at 3:10 AM, Satya Sahoo wrote:
> Hi Luc,
> We were not able to reach an agreement on how ProvenanceContainer is not a
> specialized type of Entity during our ontology call on Monday due to time
> constraints.
> To help better understand the differences and similarities, I copied the
> two definition from PROV-DM to two documents and tried to compare them
> side-by-side. The following are the two definitions:
> ===Entity====
> In PROV-DM, an entity expression is a representation of an identifiable
> characterized thing.
> ===ProvenanceContainer===
> A provenance container is a house-keeping construct of PROV-DM, also
> capable of bundling PROV-DM expressions. A provenance container is not an
> expression, but can be exploited to return all the provenance assertions in
> response to a request for the provenance of something ([PROV-PAQ]).
> According to the two definitions, a provenance container can be an
> "identifiable characterized thing" (not being an expression is not a
> conceptual constraint). Also, the ability to return all provenance
> assertions in response can be applied to an Agent also - similar to a
> software agent returning the current stock market quotes.
> Further, if an Entity "contains" provenance assertions it can still be an
> "identifiable characterized thing" thereby satisfying our current definition
> of Entity.
> During our ontology telcon today Paolo explained that the primary
> difference between Entity and Provenance Container is that Provenance
> Container can "contain" provenance assertions while Entity are assumed not
> to contain assertions. But, this seems to be an application-specific
> requirement.
> For example, for a person writing a 3-page letter the three pages will be
> instances of Entity and the envelope containing the three pages will be a
> container. But for the postal service personnel, who deal with thousands of
> envelopes per day, the envelope is an Entity (and a sack for transporting
> the envelopes will be a container).
> Hence, I believe the difference between what thing is a ProvenanceContainer
> or an Entity is an application-specific perspective/requirement and there is
> no fundamental difference between the two terms - except that Provenance
> terms seems to be a specialized form an Entity in the sense that Provenance
> Container contains provenance assertions, while an Entity may or may notcontain provenance assertions.
> Paolo suggested that we should bring up this issue to the WG mailing list -
> hence I am cc'ing the mailing list also.
> Thanks.
> Best,
> Satya
> On Wed, Sep 28, 2011 at 3:58 AM, Luc Moreau <L.Moreau@ecs.soton.ac.uk>wrote:
>> **
>> Hi,
>> I thought we had already discussed this, but I see location as subtype of
>> entity.
>> Same issue as with provenance container.  This is not a subtype of entity.
>> Luc
>> --
>> Professor Luc Moreau
>> Electronics and Computer Science   tel:   +44 23 8059 4487
>> University of Southampton          fax:   +44 23 8059 2865
>> Southampton SO17 1BJ               email: l.moreau@ecs.soton.ac.uk
>> United Kingdom                     http://www.ecs.soton.ac.uk/~lavm
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
Received on Saturday, 1 October 2011 00:12:36 GMT

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