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Re: My task from last week: Semantic free identifiers

From: Andrea Splendiani <andrea.splendiani@bbsrc.ac.uk>
Date: Mon, 20 Jun 2011 23:54:37 +0000
Message-ID: <339406501042361@jngomktg.net>
To: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Cc: "Sivaram Arabandi, MD" <sivaram.arabandi@gmail.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>, Chime Ogbuji <chimezie@gmail.com>, "andrea splendiani (RRes-Roth)" <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>
Well...
I don't think people is coding an information system by hand. Perhaps having
a look at files with just and editor happens more frequently, and I don't
think it can be avoided. 
Perhaps I'm getting the feeling that the different points of view reflects a
different perception of OWL vs RDF ?
Just a thought. I'm much more likely to move triples via scripts than using
a tool. 

ciao,
Andrea

Il giorno 20/giu/2011, alle ore 23.44, Michel_Dumontier ha scritto:

> IMHO, if you're still coding the content of an information system by hand,
then you're going to introduce errors. A database curator should never
assign their own identifier - this is internal to the technology and the
information system. If you're a programmer, you should query the resource
(ontology) for the identifiers based on the labels.  Be more sophisticated.
Do it right. Build useable APIs/UIs for people.
> 
> Best,
> 
> m.
> 
> 
> 
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
>> request@w3.org] On Behalf Of Sivaram Arabandi, MD
>> Sent: Monday, June 20, 2011 6:14 PM
>> To: M. Scott Marshall
>> Cc: Chime Ogbuji; Andrea Splendiani; MMVagnoni@mdanderson.org; James
>> Malone; HCLS; Jonathan Rees
>> Subject: Re: My task from last week: Semantic free identifiers
>> 
>> Consider the following:
>> 
>> 1. Readability - the former is far more readable than the later:
>> 	 RO:part_of
>> 		vs.
>> 	<http://purl.obolibrary.org/obo/RO_0000001>
>> 
>>    - this becomes even more apparent in a triple (CO = a 'Cardiology
>> Ontology'):
>> 	CO:Mitral_valve   RO:part_of   CO:Heart
>> 		vs.
>> 	CO_01234556   RO_0000001   CO_01234554
>> 		- doesn't make much sense (without tool support, which is
>> 'practically' non-existent).
>> 
>> 2.  Mistakes are extremely difficult to spot with opaque identifiers:
>> 	CO_01234556   RO_0000001   CO_01224554
>> 		vs.
>> 	CO:Mitral_valve   RO:part_of   CO:Brain
>> 		- this is an obviously false statement - but not easy to spot
>> if opaque identifiers were used.
>> 
>> 	This leads to a very insidious problem, one that is difficult to
>> detect.
>> 
>> 3. I am not sure why the following is an issue:
>> 	" Is my http://experiment the same as yours?
>> 	  Is my http://gene? http://study?
>> 	  Does my gene http://leads_to disease make sense?"
>> 
>> 	- Obviously if I use "http://experiment" and you use
>> "http://experiment" we both are referring to the same thing.
>> 	- But instead if I use "http://medicine/experiment"  and you use
>> "http://biology/experiment", we 'may' not be referring to the same thing.
>> 
>> 4. When using readable identifiers, it is difficult to make changes to an
>> existing term (Class) - I think this is a strength as opposed to an
issue.
>> It raises the bar and should encourage authors (of models) to create
terms
>> thoughtfully after due diligence. And when there is a real need to change
>> the term i.e. its meaning has changed or it was inappropriate, ontology
>> patterns can be used to retire the term (if necessary, labelled as
>> deprecated) or reposition it.
>> 	- 'Typos' in term names is definitely not a reason for having opaque
>> identifiers. Avoid them by having a good process for introducing terms.
If
>> and when they occur, use ontology patterns to deal with them.
>> 	- Using opaque identifiers with labels makes it very easy, almost too
>> easy, for the labels to be changed. Often times users of a model may not
be
>> aware of such changes.
>> 
>> 
>> --Sivaram
>> 
>> 
>> 
>> On Jun 20, 2011, at 4:15 PM, M. Scott Marshall wrote:
>> 
>>> 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. :)
>>> 
>>> Cheers,
>>> Scott
>>> 
>>> 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
>>> http://staff.science.uva.nl/~marshall
>>> 
>> 
>> 
>> 
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Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004
andrea.splendiani@bbsrc.ac.uk
Received on Monday, 20 June 2011 23:55:29 UTC

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