Fwd: [MOBY-l] Which machine deals with ontology issues?

[Chris Wroe]

Mark,

We have come across similar issues in myGrid and haven't yet implemented a 
complete solution.

When we built the service ontology, a 'service accepting a protein 
sequence' was considered by the classifier to be a more specific kind of 
'service accepting a sequence' because 'protein sequence' is a more 
specific kind of 'sequence'. We ended up with a nice looking classification 
but using the classification to find appropriate services caused the first 
problem you described.

If we wanted to list all appropriate services accepting a 'protein 
sequence' we returned all hierarchical descendants of 'service accepting 
protein sequence' . In fact any service accepting a sequence may be 
appropriate and services accepting more specific types may not.

A generic ontology server cannot deal with this, as it is an issue specific 
to the typing of operations. We sparked off a long debate with the logicians :)
My current view is that the directory component (or mioBoby central) should 
perform the expansion of the query to include services with more general 
input types and not those with more specific types. If they are like me, 
neither service providers or users will think of doing this on their own 
and shouldn't have to.

The second question is about a service accepting only one kind of data type 
or *any* kind of data structure that contains that type.
myGrid took the simple option. Services only accept the simple data type 
and will fail when presented with that data embedded in some more complex 
data structure. The current pre-prototype workflows included some minimal 
format transformation steps to ensure the correct fragment of data was 
passed to the next service.

The object ontology is planning for the future though! The hope would be 
that various components of the myGrid framework will in the future be able 
to interpret both ontological and XML schema datatype metadata to skim off 
appropriate elements and pass only those to the service.

Chris


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>>Date: Mon, 22 Jul 2002 10:56:52 -0600
>>
>>Hi all,
>>
>>Now that there are a handful of services up and running, the issues
>>around dealing with our wonderful Object/Service ontologies are becoming
>>clearer to me.  I'm wondering if anyone has opinions about whether
>>ontologies should be a Client/Service issue, or if they should be dealt
>>with at MOBY-Central?
>>
>>e.g. I query MOBY central with an input Object-type.  Does it respond
>>only with the services that deal with that object type, or does it track
>>down the parentage of that Object and tell me the services that deal
>>with that object type and its parents?  Similarly, does a Service accept
>>*any* type of object, and skim-off the information that it understands
>>based on the ontology, or does it restrict itself to only dealing with
>>*exactly* the type of object that it is registererd to deal with, and
>>reject everything else?
>>
>>I think these questions arise whether or not we have a separate
>>ontology-server (i.e. rip ontology-awareness out of the MOBY-Central
>>itself - which seems like a good idea in any case), as it remains
>>ambiguous who has the responsibility for dealing with the ontologies -
>>server, client, or Central?
>>
>>How does myGrid deal with this?  other opinions?  I'd like to keep
>>things as far away from the Server end as possible, since one of the
>>"founding principles" was that service-creation should be mindless... At
>>the same time, I worry that there is going to be too much pounding on
>>MOBY-Central...
>>
>>These seem like important questions which we need to address *soon*,
>>since we are already building both clients and services, and the pace at
>>which Services are appearing is increasing daily!!  Making a decision
>>now, even if it is viewed as an experiment, would be a good thing.
>>
>>M
>>
>>
>>
>>--
>>--------------------------------
>>"Speed is subsittute fo accurancy."
>>________________________________
>>
>>Dr. Mark Wilkinson, RA Bioinformatics
>>National Research Council, Plant Biotechnology Institute
>>110 Gymnasium Place, Saskatoon, SK, Canada
>>
>>phone : (306) 975 5279
>>pager : (306) 934 2322
>>mobile: markw_mobile at illuminae.com
>>
>>
>>
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Dr Chris Wroe
Clinical Research Fellow
Department of Computer Science
University of Manchester