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Re: blog: semantic dissonance in uniprot

From: Bijan Parsia <bparsia@cs.manchester.ac.uk>
Date: Thu, 26 Mar 2009 09:39:14 +0000
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <B0B592D8-0EF8-4588-A15E-6D2C686E7028@cs.manchester.ac.uk>
To: David Booth <david@dbooth.org>
On 25 Mar 2009, at 23:59, David Booth wrote:

> On Wed, 2009-03-25 at 14:13 +0000, Bijan Parsia wrote:
>> On 25 Mar 2009, at 10:41, Phillip Lord wrote:
>>
>>> "Michel_Dumontier" <Michel_Dumontier@carleton.ca> writes:
>>>> And I'm trying to explain that there is no pragmatic reason to make
>>>> explicit the distinction between a biomolecule (and what we know
>>>> about
>>>> it) and a database record (and what we know about the biomolecule)
>>>> unless they are actually different.  It just complicates things  
>>>> in a
>>>> wholly unnecessary way.
>
> There may not be a pragmatic reason for *your* applications, but there
> may well be for others, as explained below.

Yes, David, that *is* the point.

YAGNI is a good principle.

You make presumptive judgments about the "global" value of various  
rationales for different sorts of modeling without offering a serious  
cost/benefit analysis. That's fine, but it ain't rainbows and violets.

[snip]

>> This is why the the Boothian line is quite naive.
>
> Sorry, but this is not a case of naivete.

That's *soooo* cute!

> If nobody ever wants to use the same property to talk about the  
> database
> record as was used to talk about the molecule,

There, right there! Look! I *naive presumptions*.

(To wit that there is a molecule, that there is *a* molecule, that we  
know what it is, that we should optimize for a mere possibility, etc.  
etc. etc.)

[snip]
>  But if one is trying to design data to
> be reusable by others in unforeseen ways, there clearly *is* a risk  
> that
> someone will want to make such assertions in conjunction with the  
> data,
> and if that happens there is a clear harm.  This risk is easy to avoid
> by using separate URIs.

Dude, if you are going to talk about risk avoidance, you have to talk  
about *all* the risks.

You just didn't read my example. If you don't know, or can't  
reasonable determine, whether it's one *or more* molecules  
corresponding to the record, then minting *one* extra URI can embed a  
*mistake*.


> There *are* trade-offs.  Minting two URIs instead of one *does* add  
> some
> complexity, though as I pointed out that additional complexity can be
> mitigated to the point that it is a *very* low cost.

I haven't seen a persuasive and detailed cost analysis. Including  
maintenance and sanitization costs.

[snip]
> Finally, although it is flattering that you have named this suggestion
> after me, I cannot take credit.

I didn't name it, I just described it.

>  As I pointed out in my original post,
> the suggestion to differentiate between a molecule and the database
> record that describes that molecule originates with the Architecture  
> of
> the World Wide Web:
> http://www.w3.org/TR/webarch/#URI-collision
> and best practices for implementing this distinction are described in
> Cool URIs for the Semantic Web:
> http://www.w3.org/TR/cooluris

These documents, too, are systematically naive. And otherwise way out  
of touch with the Web. And contain no data.

They might contain ideas to riff off of, but they cannot be entered as  
reasonable evidence.

Cheers,
Bijan.
Received on Thursday, 26 March 2009 09:39:50 UTC

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