[MOBY-dev] registering INB services in Canada

[Oswaldo Trelles]

I'd like to provide some additional information to help understanding 
our perspective.

1) When we were developing the INB system we realise on the need for 
ensuring availability and service inter-connection based on the moby 
ontology. However, several mails from the moby community warned us on 
the importance of a curate catalogue. (i.e.) "Right now in the registry 
if I send a generic object I get over a hundred services back, almost 
none of which will actually consume the object without dying a horrible 
death." (Gordon, Feb 17th), or this other more explicit, "MOBY Central 
has become increasingly useless over the past couple of years as it got 
filled with junk, badly registered services, dead services, "localhost" 
services, test services, and all manner of other registration artifacts 
(M.W. response)"

2) In this sense we made a great effort in the registering procedure. We 
hold several internal meetings with some invited experts from the moby 
community to introduce, comment, discuss and get feedback about our 
strategy. So, it is not a new issue.
3) Natalias’s email correctly states the real-problem of different 
catalogues. In several previous emails the equivalent issues of 
federated ontologies, disperse catalogues, etc. were at least 
enumerated. So, it is opportune to launch the discussion.
4) My group at the GNV5-INB University of Malaga- is open to contribute 
in the discussion of the technical and procedural aspects involved in 
this issue, oriented to propose a global solution.
5) In our opinion, Natalia’s email is not the problem but part of the 
solution (our system works properly…at the moment at least !)

with regards,

O.

PS, I’d like to thanks all mobiers that having nothing constructive to 
say have avoided reply with unfortunate emails.

and finally I suspect that the Phillip Lord phrase regards **good** 
ontologies.



Mark Wilkinson escribió:
> 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
>>
>>
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