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Trying to summarise: Semantic free identifiers

From: James Malone <malone@ebi.ac.uk>
Date: Tue, 21 Jun 2011 20:13:18 +0100 (BST)
Message-ID: <37194.90.206.193.109.1308683598.squirrel@webmail.ebi.ac.uk>
To: "Andrea Splendiani" <andrea.splendiani@bbsrc.ac.uk>
Cc: "Helena Deus" <helenadeus@gmail.com>, "Matt Vagnoni" <matthew.vagnoni@uth.tmc.edu>, "Michel_Dumontier" <michel_dumontier@carleton.ca>, "Sivaram Arabandi, MD" <sivaram.arabandi@gmail.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>, "Chime Ogbuji" <chimezie@gmail.com>, "andrea splendiani" <andrea.splendiani@rothamsted.ac.uk>, "MMVagnoni@mdanderson.org" <mmvagnoni@mdanderson.org>, "James Malone" <malone@ebi.ac.uk>, "HCLS" <public-semweb-lifesci@w3.org>, "Jonathan Rees" <jar@creativecommons.org>
So.. a long but useful discussion. That will teach me to open my big mouth :)

Is this fair as the PRIMARY reasons for this difference in opinions:

1. Having semantic information such as a label in a URI makes it easier
to, at a glance, grasp some sort of meaning of a class/predicate and makes
SPARQLing and looking at RDF easier.

2. NOT having semantic information in a URI ensures class definitions need
to be looked up before they can be used, hence, reducing ambiguity and
that it potentially improves maintainability.

Can 1 be resolved by tooling? Seems to me 2 is happening already and will
grow as practice in a lot of the bio-ontology community. If there is a
lack of tooling surely this group should be looking at doing something
about that - funding, lobbying..

James





> Hi,
>
> I think there is some confusion going on on the subject.
>
> We need to name things in an unique way. In many cases codes are just the
> best option. No wonder we all have tax-codes and the like, it's easier
> than
> to try to find a unique name based on some attributes.
>
> The case of terminologies is an interesting case, as we need to name
> terms.
> There is a temptation to use the 'face value' of the term as a name, as
> opposed to a code. The former is clearly opening the doors for
> ambiguities,
> in this context.
>
> Beside terminologies, there are many other cases where you name thing:
>
> rdf:type
>
> owl:Class
>
> Is there a need for these to be semantically opaque ? I don't think so,
> they
> are good for mnemonics and the formal meaning is clearly defined
> elsewhere.
>
> The original thread didn't start from somebody questioning GO terms... but
> the need to replace 'partOf' with a code.
>
> To tell a funny story... I have an (unrelated) homonymous in my home town
> (which is a bit weird given the size of the town and the frequency of my
> last name). Given the identifier clash... I ended up receiving funny
> things,
> like love letters or urgent calls from unknowns... (not sure I missed some
> as well...).
> Now, when i went to register a website, which one would be better:
> mydomain/AndreaSplendiani
> mydomain/001
>
> I cannot really see any reason for the latter, and several reasons against
> it.
> Does mydomain/001 protects friend and lovers of my homonymous from
> confusion
> ? Most likely not.
>
> ciao,
> Andrea
>
>
> Il giorno 21/giu/2011, alle ore 18.46, Helena Deus ha scritto:
>
>> Other standards (outside of semantic web) saw the need to rely on
>> numeric
> identifiers, even if that created a burden for their users
>> e.g. in SNOMED Lung = T-28000
>>
>> Of course it is a pain to query SNOMED with "all the diseases that
>> affect
> T-28000".
>> But the fact is that despite the inconvenience of having to fetch that
> identifier prior to the query, SNOMED is widely used.
>>
>> What is so special about semantic web identifiers that they don't need
>> to
> follow the same path?
>
> Andrea Splendiani
> Senior Bioinformatics Scientist
> Centre for Mathematical and Computational Biology
> +44(0)1582 763133 ext 2004
> andrea.splendiani@bbsrc.ac.uk
>
>
>
>
>


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Received on Tuesday, 21 June 2011 19:14:12 UTC

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