W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > June 2007

Re: Evidence

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Mon, 18 Jun 2007 23:48:05 -0400
Message-Id: <40D488A9-906B-4D59-9B15-2399E9409359@gmail.com>
Cc: public-semweb-lifesci@w3.org
To: Pat Hayes <phayes@ihmc.us>

On Jun 18, 2007, at 1:18 PM, Pat Hayes wrote:
>> On Jun 12, 2007, at 3:53 PM, samwald@gmx.at wrote:
>>> Hi Waclaw,
>>>> Matthias, if you look carefully at BFO, you'll see that roles are
>>>> entities.  This means that evidences, as roles, are entities.
>>> Of course. I just wanted to differentiate that an experiment is  
>>> not an instance of any class called 'evidence' (in other words,  
>>> an experiment 'is not' evidence). Instead, it should be  
>>> associated with an 'evidence-role'.
>> The only problem with this is that roles inhere in continuants  
>> rather than in occurrents. One way around this is not to say that  
>> evidence is an experiment, but rather the results of an experiment.
> If I may interject, the fact that you need to find a way 'around'  
> this illustrates what I have long found to be the case, that the  
> continuant/occurrent distinction, and the resulting artificial  
> restrictions that it places upon what one is allowed to say, is  
> more harm than it is worth. One can take any ontology (such as BFO)  
> that is based up on it and simply erase the distinction (and all  
> its consequent distinctions) and nothing is thereby lost, only a  
> simplification achieved and the need for artificial work-arounds  
> diminished.

This may be true - I don't have enough experience to know whether it  
is or not. However, my comment was not  philosophically driven - it  
was simple type checking. In that ontology, for better or worse, if  
Matthias meant Role, the subclass of realizable entity, and if he  
meant that the Role was borne by a process then he should get an  
inconsistency (the fact that he would't with the current OWL version  
of BFO is to its discredit). In general, I think such type checking  
is good - my experience is that absent checks of this sort people  
just enter junk. One can't prevent them from entering junk  
altogether, but letting them know that some things are junk tends to  
get them thinking, which is a good thing.

Second from my understanding of Role (actually, any of the realizable  
entity subclasses), one would need to get some reasonable definition  
of what Role could mean if you wanted to "relax" the constraint. I  
poked and prodded the BFO folks for a while before getting some  
reasonable idea of what a Realizable Entity is and now have a good  
feel for what you need to do to define one.  An independent  
continuant having Role/Function in BFO means that the continuant has  
some potential (how much potential/likelihood is not clear) to  
participate in some process in some way. So the definition of a Role,  
in this sense, should include the thing that has the potential, the  
process in which it potentially participates in, and the way it  
participates in that process (the subProperty of has_participant).  
We've been using this definition in OBI, and it seems to be helpful  
in making people think clearly about what they are trying to say,  
which is always a good thing.

Now on reflection, evidence, even as a continuant, doesn't generally  
fit this pattern. Only in some cases involving surveillance of some  
sort is the object in question (say the recording of camera at an  
ATM) intended, before the fact, to be used as evidence. In many other  
cases it is after the fact that something observed that can be used  
as evidence. Or perhaps trivially, all things have the Role of  
evidence, in that they potentially could be used to prove something.

Now maybe Matthias meant "role" in the non BFO sense, in which case I  
would answer that I don't know what he means. What does "associated  
with an evidence-role" mean. (Maybe he can give me some definition,  
in which case we could proceed).

> It is in any case based on very debatable (and indeed debated)  
> philosophical assumptions, arising chiefly from ordinary-language  
> philosophy (and Brentano's theology) than from anything scientific.  
> It carves nature at language's joints rather than nature's joints.

Maybe it does and maybe it doesn't. Personally, I try to be aware, as  
much as possible, of how language can confuse my analytic skills -  
it's just too easy to understand by me - and demonstrably hard to  
understand by computers (of our era). Moreover cultural studies, such  
as Lakoff's work demonstrate that distinctions which we find very  
basic can be absent in other cultures, and they can make distinctions  
that we find absurd. So yes,  beware of language making you think  
there are joints where there aren't. And at the same time, I'me very  
suspicious about nature having any "joints" whatsoever. Even at the  
particle level there are controversies about what is the most basic  

I tend to look at the arguments for or against 3D/4D as off target.   
As you point out, there are  ways to interconvert. The  problem I  
have is that people say the same thing in different ways, and that  
they say them in so compact a manner that although I understand what  
follows from what they say, it is hard to find the "documentation" on  
how to do that. These problems make it too hard for me to write the  
computer programs I need to ask questions and get reasonable answers  
of collected knowledge.

So what I focus on is one one hand trying to get people (at least  
curators) to learn how to say things in same way, and on the other  
hand to figure out how to make reasonable inferences based on what  
they say. Some of those inferences can remediate cases where despite  
best efforts, they insist on talking about the same thing in  
different ways. (e.g. GO Function and GO Process are aspects of the  
same thing, something that I hope to remediate by formalizing the  
relationships between continuant, realizable entity, and process that  
I discuss above). Speaking from experience, using BFO has improved  
how well I can communicate among the people who do the same sort of  
work I do. Maybe there is something better, but there's a lot to be  
gained from going in the current direction. When we start to become  
blocked we can figure out what needs to be done then.

BTW, if you want to help in a way that would be of more direct  
impact, please consider reviewing the "proxy" relationship I proposed  
in a previous mail and tell me where it might work or not work or how  
to improve it. Or elaborate on how thinking that evidence is a  
process can help address the problems I need to deal with.

Received on Tuesday, 19 June 2007 03:48:20 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:20:27 UTC