Re: [Obi-protocol-application-branch] Fwd: cooking with ontologies

[frank g. <Fra...@nc...>]

Hi

I think we are nearly on the same page, but not quite speaking the same
language. I agree that the term ProtcolApplication along with its definition
are misleading. It is important to remember that what we define as children
of Process or ProtocolApplication are not what has been done, not what
should be done, but rather a description of/or template for what could be
done or "realised". Unfortunately both the definition of Protocol as a Plan
and ProtocolApplication do not complement each other. I also agree that
there is differences between Protocol plan and process. We can have plans
for process that are enacted, that are not enacted, and Processes which have
plans and process which have no plans. You appear to recognise this
distinction but it is not recognised in the ontology.

I am afraid I may not be able to make the call, although I may join late.
May I suggest in future we email an agenda for the call so people who cant
make it can at least comment on the points to be discussed, my points for
discussion would be

Review previous action points
Decide and at least the correct concept definition of ProtocolApplication
even if we cant agree on the correct lable
Select several use-cases
Select one-use case now to implement inside OBI
Define (by relations) what a process is
Define (by relations) what a ProtocolApplication is a result
AOB
Summaries Actions points

Sorry, this is a quickly scribbled emails

Thanks

Frank
On 3/1/07, Alan Ruttenberg < ala...@gm...> wrote:
>
> Thanks for this. Some comments:
>
> On Feb 28, 2007, at 6:41 AM, frank gibson wrote:
>
> > Final Dish, Cooking
> > Utensil and the rest are all Roles that particular Continuants play
> > in this
> > particular Cooking Occurent.
>
> Word of caution: "Role" is taken already in bfo to mean something
> which seems to differ.
> Here you use Role to mean effectively subproperties of
> has_participant. There is a discussion
> of participation in [1] starting at 290.  I'm don't think I totally
> understand the distinctions between siblings Role,
> Function, Disposition, Power, etc, but I think that it has some to do
> with the mode of participation or the type of participants.
> For example, Roles seem to be associated with only people, but that
> could either be because of agentive participation
> or because of being a kind of social animal.
>
> Anyways, for the sake of consistency, let's note that BFO uses
> "relation" for this term, and OWL uses "property" and that we should
> probably settle on one and use it consistently.
>
> > A particular recipe can be written down in a particular cook-book,
> > or in a
> > PDF, or on a scrap of paper, and in each case it is the 'same'
> > recipe (if
> > followed, would mean doing the same things to the same ingredients and
> > producing the same dish). What differs in each case is that it has
> > been
> > encoded into different media. Media is a role that (among other
> > things)
> > physical lumps of matter (a page of a book) can play.
>
> My understanding is that BFO would relate the information bits to the
> media by an inheres relationship.
> There is also this "generic dependence" that was introduced at the
> OBI workshop to capture the idea
> that the particular bits in a digital document exist by virtue of
> their being some number of physical that
> capture them e.g. 20 hard disks scattered across the world.  In any
> case, in this branch we are not really
> interested in this aspect, I think, i.e. the relation of the recipe
> to the document. Rather we are interested from
> the recipe onwards to the cooking.
>
> > Particular recipes are instances of the universal Recipy. When I
> > 'follow a
> > recipe', I am instantiating an 'enactment' relationship between the
> > particular instructions I am following and the particular activeties I
> > perform.
> >
> > In this sense, 'enactment' of a recipe is like 'running' a computer
> > program.
>
> This is a kind of "realization" in BFO. (see [1] 292).
>
> Don't know what you mean by universal recipe here.
>
> BTW, I think it is a bit muddy where the boundary of particulars and
> universals is in the realm of realizable entities.
> BS and I had a bit of discussion about this at the workshop in
> relation to some OWL prototyping I was doing for the FACS folks.
> The thing is, a particular plan can be enacted in any number of
> processes. You can cook a dish many times using the "same" recipe.
> The sense of "same" is a little ambiguous, as you could imagine
> instantiating a universal each time the recipe is followed, or
> instantiating the recipe from a class of curry recipes once and then
> cooking using it many times.  If you used the recipe as a defining
> characteristic of a class of processes, it is like the difference
> between using a nominal and class in the definition.
>
> > In OWL, we can introduce property restrictions that constrain the
> > physical
> > things or activities that can fill the different roles that would be
> > performed when enacting a recipe. That is, we could state that a
> > curry recipe
> > is any recipe where its enactment will be a process that has a
> > 'final dish'
> > role filled by some 'stuff' that is a Curry.
>
> I think we are on the same page here. So "Cytoxicity Assay" is
> "protocol" aka "plan" aka "recipe" universal, which is
> realized aka enacted as a process which have participants which are
> cells and whatever is involved in the treatment
> (called the inputs colloquially) and parts which includes
> - the a process that quantifies the number of cells (yielding
> information),
> - a process of applying a treatment and waiting
> - a process of again quantifying the number of cells.
> - a number of data transformations which finally yield a ratio which
> is the fraction of cells killed.
>
> Most likely there is also a "control" version of this process (no
> treatment/sham treatment)
> In a dose response there are a number of repetitions of this process.
>
> One of our challenges is to make clear to ourselves which terms go
> where. For example, I think
> cytoxicity assay probably belongs in protocol (plan), rather than
> process, whereas measurement of
> number of live/dead cells belongs in process. There are many reasons
> why one would measure the
> number of dead cells.
>
> Another challenge is arranging things so as to preserve appropriate
> single inheritance - either in the Rector sense (easier) or the
> Smith sense (harder, if not impossible). I'm aiming for the Rector
> sense -Where the ontology only has asserted single inheritance, but
> defined classes can lead to multiple inheritance after
> classification. "terms" that we get from the communities may land up
> either as asserted subclasses or as defined classes.
>
> Speak to you tomorrow.
>
> -Alan
>
>
>
> [1] http://ontology.buffalo.edu/smith/articles/cornucopia.pdf
>
>
>
>