W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > March 2009

Re: Less strong equivalences

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 26 Mar 2009 10:13:04 -0500
Cc: eric neumann <ekneumann@gmail.com>, Bijan Parsia <bparsia@cs.manchester.ac.uk>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <37B22BCD-FC2E-4565-B61B-217ACE48F23F@ihmc.us>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>

On Mar 26, 2009, at 7:16 AM, Phillip Lord wrote:

> Pat Hayes <phayes@ihmc.us> writes:
>>> From your descriptions, I can't tell which one would best handle the
>>> following situation:
>>>
>>> "Object 1 refers to exactly the same molecule (exemplar) as object  
>>> 2 refers
>>> to"
>>
>> That sure sounds like sameAs, applied to molecules. Why isn't  
>> sameAs good
>> enough here? What goes wrong?
>
> I can think of very few occasions when we want to talk about a  
> molecule

First lets be clear, by 'molecule' I didnt mean one very small piece  
of matter. I meant, whatever was meant by "molecule" in "applied to  
molecules" in what I was responding to. I presume this means something  
like 'molecular structure'. This kind of type/token distinction is  
common in many fields (books versus works, species versus individual  
animals, etc.) and we ought to have no problem with it here.

> ;
> we need to talk about classes of molecules.

That is simply not obvious. Lets not jump into deciding what is a  
class and what isn't. I don't recommend treating a molecular structure  
as a class of molecules.

> We can consider this as
> problematic even with a very simple example.
>
> Let's assume we have two databases with information about Carbon.

meaning, I presume, the element with atomic number 14.

> Do we
> use "sameAs" to describe the atoms that they are talking about?

If it is clear we are not talking about individual molecules, yes.  
Chemists have the notion of 'element' for just this purpose.

> Maybe,
> but what happens if one is talking about the structure of Carbon and
> it's location in the periodic table, while the other is talking about
> Carbon with the isotopic mix that we have in living organisms on  
> earth?

So what? They can be saying different things about the same element.  
Any isotopic mix of carbon is still carbon. If you wanted to  
distinguish different isotopic mixes as distinct kinds of thing, then  
you should have said so: in that case, maybe sameAs isn't appropriate  
in this example, because (with that understanding of what we are  
talking about) the two databases aren't about the same thing.

>
> In biology, we have the same problem. Is porcine insulin the same as
> human insulin? Is "real" human insulin the same as recombinant
> human insulin? Well, the answer to all of these is no

Fine, you just answered the basic ontological question.

> , even though most
> biologists will tell you that real and recombinant insulin are the  
> same
> because they have the same primary sequence; a medic will tell you
> otherwise, because they have different effects. Why? Don't know.

A deep question, but not a killer for ontology use.

>
> If you make the distinctions that you might need some of the time, all
> of the time, then you are going to end up with a very complicated  
> model.

Yes, you no doubt are. Tough. Its a complicated world. Formal  
ontologies are often, perhaps always, more complicated than the  
informal 'knowledge' they set out to formalize. They are obliged to  
make finer, more persnickety, distinctions between things.

> Hence the evolutionary biologist says all the insulins are the same.

I don't care what the anyone says, that is wrong. They are  
indistinguishable for certain purposes, but if anyone can distinguish  
them at all, they are not the _same_.

> The
> medic says that they are different. And neither of them care about
> different types of carbon (unless they are C14-dating).
>
> I don't think that there is a generic solution here which is not too
> complicated to use.

All these examples can be handled by making fussy distinctions between  
kinds of thing at different granularities: carbon molecules, carbon  
isotopes, carbon the element; and then having mappings between them.   
I don't know much about insulin, but it sounds from the above that the  
same trick would work. It is tedious and hair-splitting to set this  
up, but once in place its fairly easy to use: you just choose the  
terminology corresponding to the 'level' you wish to be talk ing  
about. sameAs works OK at each level, but you can't be careless in  
using it across levels.

If this makes you want to groan, I'm sorry. But ontology engineering  
is rather like programming. It requires an unusual attention to detail  
and a willingness to write a lot of boring stuff, because its for  
computers to use, and they are as dumb as dirt and have to have every  
little thing explained to them carefully. And yup, its complicated.  
Until AI succeeds, it will always be complicated.

> The only solution (which is too complicated) I can
> think of is to do what we do when we have this problem in programming;
> you use a pluggable notion of equality, by using some sort of  
> comparitor
> function or object. I don't think that this is an issue for OWL  
> myself;
> I think it's something we may need to build on top of OWL.

It belongs in your ontology for carbon and insulin, not in OWL.

Pat

>
> Phil
>
>
>

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Received on Thursday, 26 March 2009 15:14:54 UTC

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