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Re: My task from last week: Semantic free identifiers

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Mon, 20 Jun 2011 22:15:22 +0200
Message-ID: <BANLkTi=V7W2MOHtRxLw9UFvMmBYMc8qZeQ@mail.gmail.com>
To: Chime Ogbuji <chimezie@gmail.com>
Cc: Andrea Splendiani <andrea.splendiani@bbsrc.ac.uk>, MMVagnoni@mdanderson.org, James Malone <malone@ebi.ac.uk>, HCLS <public-semweb-lifesci@w3.org>, Jonathan Rees <jar@creativecommons.org>
Hi Chime,

The main reason is that when semantics and natural language are
inserted into identifiers, some identifers are doomed to become stale
as thinking evolves or changes about the semantic representation. Or
when a new 'name brand' is created for that namespace: I think that
the best example of this was provided by Jonathan Rees for Shared
Names - ever heard of 'locuslink' identifiers? I believe that Entrez
Gene occupies the name branding of that space now.This is precisely
the sort of problem that Shared Names would like to avoid by serving
(non-ontological) identifiers from a 'neutral namespace'. In
ontologies, the same principle applies (I see that Helena has supplied
a good example).

I agree with Mark about proper tooling - the tools should
automatically display labels. It's true that I don't know of a SPARQL
editor that does this to a satisfying degree yet, (except for one:
SPARQL Assist Lanugage-Neutral Query Composer from McCarty et al,
shown at SWAT4LS in Berlin :) See Mark's post.) but that is not a
reason to create identifiers and your knowledge representation in a
way that won't stand the test of time.

Shouldn't we consider RDF to be the bytecode of knowledge? Although I
understand the difficulty of dealing with non-human readable
identifiers in SPARQL and RDF, I believe that we are now looking at
bytecode and complaining that it isn't human readable. It's true that,
until the tools are available, it is difficult to write SPARQL
queries. But if we applied the same logic to gene accession numbers,
where would we be now? The SPARQL queries will eventually be 'under
the hood', supplying labels to a GUI near you. :)


On Mon, Jun 20, 2011 at 9:34 PM, Chime Ogbuji <chimezie@gmail.com> wrote:
> On Monday, June 20, 2011 at 3:08 PM, Andrea Splendiani wrote:
> Hi,
> sorry to jump on this thread like this...
> To be honest, I'm kind of concerned by the insistence on semantic-opaque
> identifiers.
> I am as well and I have been for some time.
> I understand the reason for them,
> Actually, I would be interested in hearing the reason for them enumerated,
> because I have had a hard time imagining what could possibly offset the
> (significant) impact on readability that it has on biomedical ontologies.
>  The barrier is already high for non-logicians and non-semantic web
> aficionados to use biomedical ontologies.  Why set it any higher?
> -- Chime

M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
Received on Monday, 20 June 2011 20:15:59 UTC

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