Re: blog: semantic dissonance in uniprot

I think this discussion has been quite useful and important, since there are
some remaining issues to be clarified by this community. I think all points
raised are good, but not equally valid. Bijan and Phil's thoughts are very
useful for me, and would probably resonate within the informatics groups at
pharma companies.

I think a key guidance principle here is to ensure that whatever is proposed
"makes sense and works with molecular biologists" (scientists). Perhaps
existing information resources need a major "enhancement" in order to work
in a semantic web, but then let's make it quite clear (to all possible
users) what the readily perceivable value of all these ontological
adjustments will be.

cheers,
**Eric


"Ceci n'est pas une *protéine !**"** **- with apologies to René Magritte*



On Tue, Mar 24, 2009 at 9:01 AM, Kingsley Idehen <kidehen@openlinksw.com>wrote:

> Bijan Parsia wrote:
>
>> On 24 Mar 2009, at 05:06, Kingsley Idehen wrote:
>> [snip]
>>
>>> Michel,
>>>
>>> 303 redirection serves a single purpose: enforcement of the Identity
>>> principle for discrete data objects. If a datum lacks identity it cannot in
>>> away be resourceful.
>>>
>>
>> Identity principle? Resourceful? What is it to be resourceful?
>>
>> In general (i.e., in the broadest context) the identity conditions of data
>> objects typically is not their name. E.g., consider lexical form and
>> xsd:integer.
>>
>>  The identity principle also implies that "Identity" stands alone from all
>>> else, you cannot intermngle with "representation", for instance.
>>>
>> [snip]
>>
>> I strongly recommend not appealing to potentially tendentious and hard to
>> explicate, much less empirical support, principles in these discussions. One
>> is more likely to communication across conceptual perspectives if one
>> operationalizes one's concepts.
>>
>>  If you are going to honor the Identity principle on the Web,
>>>
>>
>> There's no honor among engineers.
>>
>>  in an unobtrusive manner (i.e., leverage ubiquity of HTTP) there is no
>>> way around the above.
>>>
>>> The whole essence of the Linked Data Web comes down to distillation of
>>> Data Objects from the host Information Resources (documents) i.e, making the
>>> Data Objects
>>>
>>
>> These captializations scare me.
>> [snip]
>>
>>> Scientist are always preoccupied with,
>>>
>>
>> I'm a scientist! I'm not always so preoccupied with database records!
>> Except DBLP!
>>
>>  and interested in, database records because science lives and dies
>>>
>>
>> By funding!
>>
>> By publications? Backstabbing? Politics? Grad students and postdocs? Am I
>> warm?
>>
>>  by the following processes:
>>>
>>
>> Damnit! I got it wrong AGAIN! ;)
>>
>>  1. Hypothesis
>>> 2. Observation
>>> 3. Conclusion
>>>
>>
>> Tendentious (and very naive) philosophy of science seems poor ground upon
>> which to sprout the tree of  Engineering Consensus!
>>
>> Seriously, there's a huge, rich literature about the nature and practice
>> of science. Very little of it would embrace this description even as a crude
>> formulation.
>>
>>  The steps above are about units of observation ("data"), contextual
>>> representation ("information"), and conclusions ("knowledge").
>>>
>>
>> Such scare quotes are scary! I don't know what a "unit" of "observation"
>> is, but the history of such concepts as observation sentences in Carnap
>> doesn't leave me with much hope.
>>
>> So, at this point, I can't distill out your position, much less how all
>> this is supposed to support that position. Is it really necessary? Aren't
>> there simpler, more direct considerations?
>>
>>  In my experience, scientists are completely preoccupied with Data :-)
>>>
>>
>> Well, I hope I've now embiggened your experience!
>>
>> Cheers,
>> Bijan.
>>
>>  Bijan,
>
> Is "Identity" important or not? That's the question here.
>
> Is granularity important or not? A variation of the statement above.
>
> 303s are just about "Identity" at the datum level within the context of the
> Web when using a particular form of HTTP based URI scheme (the Slash based
> URI).
>
> Should we be able to reference a datum and de-reference a representation of
> its description via the Web?
>
>
> --
>
>
> Regards,
>
> Kingsley Idehen       Weblog: http://www.openlinksw.com/blog/~kidehen
> President & CEO OpenLink Software     Web: http://www.openlinksw.com
>
>
>
>
>
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