Re: [Obo-relations] [bfo-discuss] Incorporation of RO relations into BFO, and future development of RO
Lindsay G Cowell
> The attached bottle2.graffle.pdf shows the last state of the
> discussion and the proposed relations among parts. A point of mystery
> for me is the claim that the coin not located nor contained in the
> water.
That actually seems intuitive to me. It seems the coin is surrounded by the water the way we are surrounded by air. It doesn't seem right to use located or contained in with any fluid as the site/container (i am probably using site wrong here).
Lindsay
>
> Regards,
> Alan
>
>
> >
> > Best regards
> > Stefan
> >
> > 2010/5/26 Larry Hunter <Larry....@ucdenver.edu>:
> >>
> >> On May 26, 2010, at 1:35 PM, Chris Mungall wrote:
> >>
> >>> We propose that the next version of BFO will contain a minimal set of
> >>> instance level binary relations -- this set will overlap with the set
> >>> of instance level relations used in the original RO.
> >>
> >> Chris,
> >>
> >> This is wonderful news. We will review this proposal and submit comments.
> >>
> >> I was wondering if the Özgövde andl Grüninger paper from FOIS
> this year ("Foundational Process Relations in Bio-Ontologies")
> influenced the proposal? Their FOL characterization struck me as
> potentially very useful.
> >>
> >> Larry
> >>
> ------------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> Obo-relations mailing list
> >> Obo-re...@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/obo-relations
> >>
> >
> >
> >
> > --
> > Stefan SCHULZ (apl. Prof. Dr. med.)
> > Institute of Medical Biometry and Medical Informatics
> > University Medical Center Freiburg
> > Stefan-Meier-Strasse 26 79104 Freiburg (Germany)
> > [home: Eschholzstr. 70, D-79115 Freiburg]
> > +49 (0)761 2036725, 2049089
> > http://purl.org/steschu
> > [stsc...@uni-freiburg.de], Skype: stschulz
> >
> > --
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> [attachment "Bottle2.graffle.pdf" deleted by Lindsay G
> Cowell/BioStat/mc/Duke]
Colin Batchelor
> That actually seems intuitive to me. It seems the coin is surrounded by
> the water the way we are surrounded by air. It doesn't seem right to use
> located or contained in with any fluid as the site/container (i am probably
> using site wrong here).
Yes.
The air resists my movement and the water resists the coin's movement, but not very hard, and not really enough to change the outer edge of the air/water very much.
Imagine, though, that you are in a giant wet paper bag and I am in a giant hamster ball.
These are intuitively both cases of containment.
But if you press against the wet paper bag, even not very hard, you tear it open, and if I press against the hamster ball, then it rolls in the direction I push it.
Best wishes,
Colin.
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Alan Ruttenberg
>
>> The attached bottle2.graffle.pdf shows the last state of the
>> discussion and the proposed relations among parts. A point of mystery
>> for me is the claim that the coin not located nor contained in the
>> water.
>
> That actually seems intuitive to me. It seems the coin is surrounded by the
> water the way we are surrounded by air. It doesn't seem right to use
> located or contained in with any fluid as the site/container (i am probably
> using site wrong here).
Just to continue testing your intuition.
1) Suppose the coin is buoyant and floats in the middle of the water
2) Suppose the coin has control of where it can go - it can be in the
water or hover above it
3) Suppose the body of water is bigger - a bathtub, a lake, an ocean.
When, if ever is the coin located in the body of water. (are
submarines "in" the atlantic ocean not "located in" the atlantic
ocean?.
-Alan
Alan Ruttenberg
> Lindsay Cowell writes:
>
>> That actually seems intuitive to me. It seems the coin is surrounded by
>> the water the way we are surrounded by air. It doesn't seem right to use
>> located or contained in with any fluid as the site/container (i am probably
>> using site wrong here).
>
> Yes.
>
> The air resists my movement and the water resists the coin's movement, but not very hard, and not really enough to change the outer edge of the air/water very much.
>
> Imagine, though, that you are in a giant wet paper bag and I am in a giant hamster ball.
>
> These are intuitively both cases of containment.
Though containment as intended in ro1 was meant to be between the
*interior of* the bag/ball and you.
-Alan
ps. what's a hamster ball?
>
> But if you press against the wet paper bag, even not very hard, you tear it open, and if I press against the hamster ball, then it rolls in the direction I push it.
>
> Best wishes,
> Colin.
>
> DISCLAIMER:
>
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------------------------------------------------------------------------------
Colin Batchelor
> ps. what's a hamster ball?
http://en.wikipedia.org/wiki/Hamster_ball or http://en.wikipedia.org/wiki/Zorbing
Colin.
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Lindsay G Cowell
> >> The attached bottle2.graffle.pdf shows the last state of the
> >> discussion and the proposed relations among parts. A point of mystery
> >> for me is the claim that the coin not located nor contained in the
> >> water.
> >
> > That actually seems intuitive to me. It seems the coin is surrounded by the
> > water the way we are surrounded by air. It doesn't seem right to use
> > located or contained in with any fluid as the site/container (i am probably
> > using site wrong here).
>
>
> Just to continue testing your intuition.
>
> 1) Suppose the coin is buoyant and floats in the middle of the water
> 2) Suppose the coin has control of where it can go - it can be in the
> water or hover above it
> 3) Suppose the body of water is bigger - a bathtub, a lake, an ocean.
> When, if ever is the coin located in the body of water. (are
> submarines "in" the atlantic ocean not "located in" the atlantic
> ocean?.
I would say the coin is *in* water, but i don't think I would say it is *located in* water or *contained in* water. Location to me implies position like longitude/latitude so the use of spatial regions makes sense. With the submarine example, we might say informally that it is located somewhere in the atlantic ocean, but what we really mean, i think, is that the coordinates of the submarine's location are also coordinates of the atlantic ocean. (I am ignoring all sorts of complications here, but trying to account for them would just drown the point.)
Lindsay
Alan Ruttenberg
I think we need a relation corresponding to "in", since people seem to
make that judgment more consistently than the current located in and
contained in.
-Alan
Ward Blondé
> I think we need a relation corresponding to "in", since people seem to
> make that judgment more consistently than the current located in and
> contained in.
>
Ward
Ms. Meena Kharatmal
>
>> I think we need a relation corresponding to "in", since people seem to
>> make that judgment more consistently than the current located in and
>> contained in.
>>
> What about 'is in'? :-)
my only worry is that 'is in' does not create problems as the link 'is
a' had in terms of ambiguity.
inorder to be precise we may need to use 'is located in' or 'is
contained in' whereever applicable.
Meena.
--
"I link, therefore I am"
......................................................
Meena Kharatmal
blog --> http://okeanos.wordpress.com
twit --> http://twitter.com/meena74
web --> http://www.hbcse.tifr.res.in/~meena
......................................................
Alan Ruttenberg
>
>> I think we need a relation corresponding to "in", since people seem to
>> make that judgment more consistently than the current located in and
>> contained in.
>>
>
> What about 'is in'? :-)
Well that settles the name. All we need is a definition ;-)
-Alan
Alan Ruttenberg
<alanrut...@gmail.com> wrote:
> On Fri, May 28, 2010 at 3:47 AM, Ward Blondé <ward....@ugent.be> wrote:
>>
>>> I think we need a relation corresponding to "in", since people seem to
>>> make that judgment more consistently than the current located in and
>>> contained in.
>>>
>>
>> What about 'is in'? :-)
>
> Well that settles the name. All we need is a definition ;-)
One definition that we could use, is slightly more general that
g-containment in the Maureen's paper -
x in y iff convex hull of x part of convex hull of y.
I don't use g-containment because it makes use of R() in the
definition and I've mentioned my difficulty in understanding how R
works in all cases. It does, however, implicitly, understand that
there are regions though perhaps there is a formulation of convex hull
containment that can be made without resort to spatial regions. If you
allow only lines between parts of entities, then a in b means any line
between two parts of a is part of a line between two parts of b.
-Alan
Colin Batchelor
> One definition that we could use, is slightly more general that
> g-containment in the Maureen's paper -
>
> x in y iff convex hull of x part of convex hull of y.
Consider Achille Varzi(I think it is)'s wine glass (only works in monospaced fonts, sorry):
\ /
\ /
|*
|
~~~~~
The * is a fly. It's buzzing around in the convex hull of the glass but is not in the glass in any intuitive sense.
Using the natural-language sense of the word "in" rather will probably lead to the same kind of problems that logicians found with the natural-language senses of "and" and "or".
Other difficulties that occur to me: water in a very full glass where the meniscus points upwards. Water within the meniscus is excluded from being in the glass by the definition above. Equally if I'm in a sleeping bag with my head sticking out.
The convex hulls of drug molecules binding with target proteins aren't necessarily within the convex hull of the protein.
Best wishes,
Colin.
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Alan Ruttenberg
> Alan Ruttenberg writes:
>
>> One definition that we could use, is slightly more general that
>> g-containment in the Maureen's paper -
>>
>> x in y iff convex hull of x part of convex hull of y.
>
> Consider Achille Varzi(I think it is)'s wine glass (only works in monospaced fonts, sorry):
>
> \ /
> \ /
> |*
> |
> ~~~~~
>
> The * is a fly. It's buzzing around in the convex hull of the glass but is not in the glass in any intuitive sense.
The fly is in the wine glass in the same way that a peptide is in the
groove of an MHC molecule, no?
The question isn't necessarily whether the relation perfectly tracks
natural language - none of the ones proposed so far does. But among
the ones that don't, I'd say we're aiming for ones that a) Minimize
how often this sort of thing happens, and b) Can be applied in a
consistent way.
I'd argue this one is comparable to the others on a) and wins on b)
-Alan
Colin Batchelor
> The fly is in the wine glass in the same way that a peptide is in the
> groove of an MHC molecule, no?
Correct.
But what we need, and what I haven't seen in this discussion yet, is:
(a) a catalogue of situations like the fly in the wine glass, the peptide in the groove of an MHC molecule, a dog sticking its head out of a car window, _and_ the *entailments* that you want to get out.
(b) somebody to explain what's wrong with regions.
Albert Goldfain
<alanrut...@gmail.com> wrote:
>
> I think we need a relation corresponding to "in", since people seem to
> make that judgment more consistently than the current located in and
> contained in.
>
I'm sure you have been asking for the judgments of English
speakers...because had you asked for the judgments of Atsugewi
speakers, you would have found 18 different lexicalizations of "in"
and "into" that we don't have in English (see pdf pages 17-19 in this
work by Talmy: http://www.cog.jhu.edu/faculty/smolensky/050.341-641/Readings/Talmy%2000%20chap3.pdf
), including individual words for:
"into an aerial enclosure"
"into a gravitic container" (i.e., something with a bottom)
"into a fire"
"into an aggregate"
English was built for Science, but Atsugewi was built for describing
the nuances of containment...do bad we're stuck with "in" :)
-Albert
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