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Re: Advancing translational research with the Semantic Web

From: Pat Hayes <phayes@ihmc.us>
Date: Tue, 29 May 2007 10:28:40 -0700
Message-Id: <p06230916c2820c99e095@[]>
To: Alan Rector <rector@cs.man.ac.uk>
Cc: Phillip Lord <phillip.lord@newcastle.ac.uk>, Marijke Keet <keet@inf.unibz.it>, public-semweb-lifesci@w3.org

>On 21 May 2007, at 19:50, Chris Mungall wrote:
>>On May 20, 2007, at 11:49 PM, Alan Rector wrote:
>>>On 18 May 2007, at 18:10, Chris Mungall wrote:
>>>>I'm afraid I'm unclear how to state the OWL n-ary relation 
>>>>pattern(http://www.w3.org/TR/swbp-n-aryRelations) where I really 
>>>>need it. In all the examples given, the "lifted"[*] n-ary 
>>>>relation was never truly a relation in the first place and always 
>>>>better modeled as a class. It's kind of cheating. What if my 
>>>>n-ary relation is transitive or if the 3rd argument is a temporal 
>>>>interval over which the relation holds?
>>>>I think the former is doable with property role chains. Updating 
>>>>the n-ary relations note with this - and all the other omitted 
>>>>details, such as how to re-represent domain/range, functional 
>>>>properties, n-ary relations in restrictions etc - would take a 
>>>>lot of work and would make it utterly terrifying to the naive 
>>>>Nevertheless the results are clunky and will need special tool 
>>>>support[**] to avoid going insane.
>>>I'd love to see DLR or similar means worked into future versions 
>>>of OWL or other standards, although I am not the one to comment on 
>>>the logical/complexity issues.   I certainly agree that 
>>>re-expresssing relations as properties carries a modest penalty by 
>>>being more verbose, but it is manageable.
>>>To take the example in question for some relation R, let's take 
>>>temperature as an example.  I shall use the subrelations 
>>>"has_feature" / "has_state" to minimise arguments over what is, 
>>>and is not a "quality" - an issue not germane to this discussion. 
>>>Also I will use "has_state" as the property name so we don't have 
>>>both a property "has_value" and a keyword VALUE.
>>>In the binary relation form in manchester simplfied syntax in OWL 
>>>1.0 we have:
>>>Organism has_feature SOME (Temperature_Feature THAT
>>>         has_temporal_extent VALUE temporal_extent_1 AND
>>>         has_state SOME (has_magnitude VALUE 37 AND has_units VALUE 
>>>where temporal_extent_1 is an individual which has facts
>>>	has_start_time VALUE n AND has_end_time VALUE m.
>>>	has_magnitude is a functional datatype property and has_units 
>>>is a functional property.
>For the record, I accidentally left this ambiguous as to whether it was
>"Organisms that a temperature of 37C during temopral extent 1"
>	Organism THAT has_feature. SOME (...
>or the claim, better as
>"This class of organism has the temperature feature during  temporal extent 1"
>	"ThisOrganismClass --> has_feature SOME (...
>Should be
>>Here Temperature_Feature is a "history" (sensu Hayes) or a 
>>time-slice. Do I have this correct?
>Deliberately left ambiguous to limit the number of cardinaltiy 
>constraints to explain.  It depends on the cardinality of 
>is_feature_of.   I had not put a max 1 cardinality constraint on it, 
>implying that there can be many features, but any feature at any 
>time.  For most purposes the inferences are the same.  However, to 
>expand the example.
>If you want features to be 4-D objects

Just for the record, that IS the 'histories' view. That is, 
'histories' was the name I used for 4-d objects.

>that have values at a time,

However, 4-d objects don't have values *at a time*, since they have 
time built into them. They are objects-at-a-time, and they simply 
have values. If they weren't objects-at-a-time, they wouldn't be 4-d.

>Let's go back to basics.
>What is the statement in plane English? I presume:
>"A protein that is located in some cytoplasm during some temporal extent"
>What inferences do you want to draw about the Protein? the Cytoplasm?

As usual with a robust call to plain old English, it is no longer 
clear what we are talking about. What ARE these entities? 
Continuants? Occurrents? Do they extend through time? Do they have 
temporal parts? Do they have spatial parts?

>the History of each?

In the 4-d view, these things (in fact, everything that exists in 
space-time) IS a history. Histories do not 'have' histories. (The 
idea of a thing having a history, and the two of them being 
inherently distinct, is a hallmark of the continuants notion, where 
continuants aren't allowed to have temporal parts. Unfortunately, 
this continuant/occurrent distinction has been welded into BOF and 
DOLCE and so has become very influential.)

>What inferences do you wish to make that you cannot make from the 
>simpler representations?
>What else do you need to say that can be expressed with Histories 
>that cannot be expressed in the simpler representation?

Seems to me that histories is a simpler representation. It treats all 
spatiotemporal entities uniformly, and does not require maintaining a 
distinction between continuant things and occurrent 
lifetimes-of-things, for example. All it amounts to in practice is to 
be rigorous about the idea that (expressed in terms familiar to 
occurrent/continuant philosophy) everything is an occurrent, so 
everything has temporal parts. Even continuants are occurrents :-) 
Temporal parts can then be simply related to one another without 
being concerned with where to put the temporal parameters, etc.. So 
in this example, the relation between the protein-during-extent and 
the cytoplasm-during-extent (both temporal parts of protein and 
cytoplasm, respectively) is simply located-in, with no temporal 
qualification at all. Since all part-of relations, temporal or 
spatial, are binary, this fits very well into the OWL world of binary 
properties. One way to do it for example is to treat a time-interval 
as a property on things whose value is the relevant temporal part of 
that thing. Of course, this isn't how we speak in English, which is 
no doubt why many people find it confusing at first; but one can 
treat this simply as a matter of translation of surface form. To say 
that (say) A is inside B during interval I, is a compact way of 
saying A-I is inside B-I; or using the convention suggested above, 
that the I-value of A is inside the I-value of B. Humans prefer the 
more compact representation, which is fine. But what best fits the 
human left temporal lobe is not necessarily best for machines to 
reason with. And in any case, as I myself can attest, it does not 
take long to get used to the 4-d way of thinking. Assuming of course 
that I am human.


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Received on Tuesday, 29 May 2007 17:28:55 UTC

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