[MOBY-dev] registering INB services in Canada

[Mark Wilkinson]

The immortal words of Phillip Lord are ringing in my head right now... "An  
ontology is not an ontology unless it is SHARED!" :-)

This is a topic that has been discussed (perhaps not on-list?) for many  
years - going all the way back to the first group (PlaNet) who set up  
their own registry.  If you "fork" the ontology, then everything breaks,  
unfortunately.  I don't think we have ever found a workable solution to  
this situation.  Next-generation MOBY, with RDF/OWL and reasoning and  
such, may be able to deal with this problem, but MOBY-S is pretty much  
stuck with one, centralized ontology (which, in our defence, is how the  
vast majority of ontologies work at this point in Web history).

I'm just catching up with my emails after being away for 10 days.  I don't  
see anyone else responding to this so far.  I don't have any suggestions  
to help you at the moment, but I can raise it at my next lab meeting and  
perhaps an idea will come up...??  I have a feeling that there isn't a  
"magic" solution.  MOBY works *because* we all agree on the ontology.  If  
you don't agree on the ontology, then you aren't interoperable... it's  
pretty much the core principle of the project...

M




On Thu, 07 Dec 2006 03:04:47 -0800, Natalia Jimenez Lozano  
<natalia.jimenez at pcm.uam.es> wrote:

> Hi,
>
> I would like to open a discussion about ontologies. I belong to the INB
> where we have currently a lot of working services. We would like to
> register all of our services in Canada but due to the differences
> between both ontologies (Canada and Spain), we could ran into the
> following problems:
>
> a) Identical objects (objects that share the same name and the same
> hierarchy): in this case there would be no problem using the object
> previously registered in Canada.
>
> b) Analogous objects (objects that share the same name but different
> hierarchy): it would be possible to register in Canada the object with
> the same name but different hierarchy? If it would be possible we would
> be "breaking" the Canadian ontology :-(
>
> Some examples of this situation can be easily found:
>
>     b.1. NCBI_BLAST_Text: in Spanish ontology, this object is a son of
> text_formatted node but in Canadian ontology is a son of BLAST-Report
> that is at the same time a son of Sequence_alignment_report.
>     b.2. There is a lot of common objects like Clustalw_Evaluated_Text,
> FASTA, GFF ..., etc which only difference is their depencency: in
> Canadian ontology, these objects are depending on text-formatted node
> but in the Spanish ontology on text_formatted (the only difference is
> hyphen/underscore!).
>
> c) Similar objects (different name -similar, upper-case/lower case,
> underscore/hyphen- and/or different hierarchy but same meaning): to fit
> to this last situation, we have several options:
>
>     - To register INB objects -> this would not "break" the Canadian
> ontology but would "blur" it.
>     - To adjust each one of the INB services to the Canadian ontology ->
> This would mean the modification of the code of each one of the services
> and it would require an extra work.
>     - To modify INB ontology to adjust to Canadian ontology -> This
> would be a thorny issue because since INB beginnings we have work very
> hard in this sense. Even we organized an ontology committee to give
> advise on each new object to be registered. Moreover, few months ago we
> restructured our ontology with the aim of removing inconsistencies. In
> my opinion, we have currently a very solid ontology.
>
> Suggestions about how to register INB services in a easily and not
> damaging way?
> Thank you very much in advance,
> Regards,
> Natalia
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Using Opera's revolutionary e-mail client: http://www.opera.com/mail/