[MOBY-dev] Re: Service Ontology developments

Mon Apr 19 18:55:00 UTC 2004

Hi Phil,

Many thanks for your excellent comments. Im in agreement with you on 
the issue of using the MyGrid ontology, I think the hope would be that 
we could use branches of it or establish mappings between appropriate 
parts of MOBY and MyGrid ontologies so that the two systems could talk 
each other's language where appropriate. Definitions for the MyGrid 
ontology would be really nice - do they live somewhere that I can find 
them?

I look forward to any other thoughts you have on the structure so far.

Cheers,

	Simon.

On Apr 19, 2004, at 10:57 AM, Phillip Lord wrote:

>
>>>>>> "Simon" == Simon Twigger <simont at mcw.edu> writes:
>
>   Simon> Hi there,
>
>   Simon> Following the MOBY meeting a few weeks back, I've started to
>   Simon> sketch out a service ontology structure as a basis for
>   Simon> discussions - Im sure it will get kicked around and reworked
>   Simon> but thats the goal. I've committed some things to the
>   Simon> moby-live repository in moby-live/Docs/ontologyDevelopment/
>
>
>   Simon> Given the S-MOBY direction of going to OWL and needing a
>   Simon> decent editor and some practice with these things, I've been
>   Simon> putting this together using Protege in OWL format. If we need
>   Simon> to convert to something else, thats fine but its a reasonable
>   Simon> place to start and Protege is a nice tool with the OWL plugin
>   Simon> and the OWLviz graph add-on. If you open up the .pprj file in
>   Simon> Protege you will be able to read the service descriptions,
>   Simon> etc. which will help understand what I thought they all did.
>
>
> The OWLViz plug-in was written by people, here, at Manchester. So if
> you start using it please give me a shout; they would welcome the
> feedback.
>
>
>   Simon> I went through Emboss and Pise and tried to use those tools
>   Simon> to guide the types of classes we should have -
>
> If you have not already, then its worth having a look at the EMBOSS
> ACD type system.
>
>
>   Simon> I dont think they all will fit in what I have now but its a
>   Simon> start. I looked at the MyGrid ontology and the reasoned
>   Simon> version courtesy of Phil Lord and the power of being able to
>   Simon> reason over the ontology is well worth considering and this
>   Simon> was another reason I went with OWL (you can attach the Racer
>   Simon> reasoning engine very easily).
>
>
> <partisan>
> Or, of course, the wonderful FaCT reasoner.
>
> http://www.cs.man.ac.uk/~horrocks/FaCT/
> </partisan>
>
>
> Hopefully there should be a new version of fact out soon, which does
> some things quite a bit quicker.
>
>
>
>
>   Simon> Their ontology is much more fully formed but that is the
>   Simon> nature of DAML/OIL and OWL - you are trying to describe your
>   Simon> 'knowledge space' and the hierarchical ontologies we have in
>   Simon> MOBY right now are a very simple structure in comparison (but
>   Simon> on the flip side, they are useable now!). Now I understand
>   Simon> things a little more, there is much in the MyGrid ontology
>   Simon> that we might want to use/copy/refer to. Im not yet at the
>   Simon> point of being able to say if we should adopt it wholesale,
>   Simon> that is a much larger issue but we all want to avoid
>   Simon> reinventing these wheels.
>
>
> My own feeling, which may surprise you, is that you should not adopt
> the ontology wholescale. Currently, I think the ontology is too big,
> and somewhat confusing to use. Within an end user tool, you would need
> to document all the concepts. And there are quite a few of them.
>
> Within mygrid our intention would not be to present the entire
> ontology to the end user, but chunks of it. It's not really possible
> to make this split in moby-s as it stands; at least not to my
> knowledge.
>
>
>   Simon> Key things for us to look at as I see it, bearing in mind
>   Simon> I've only been looking at this for a few weeks:
>
>
>   Simon> Development path - do we want to have some simple,
>   Simon> incremental additions to our current Service Ontology so we
>   Simon> can better classify services for MOBY-S or are we looking to
>   Simon> make a quantum leap towards a more comprehensive ontology in
>   Simon> OWL that is leading towards S-MOBY in the future, or more
>   Simon> likely, both of these options?
>
> If you want to go for OWL, in a way which enables you to reason, then
> you would need to think a fair bit about the ontology API which is not
> really up to it yet. It would also mean that you would have to tackle
> events like the ontology becoming inconsistent.
>
>
>
>
>   Simon> Structure of the ontology - I've be wresting with naming and
>   Simon> how to partition services that obviously do more than one
>   Simon> thing. Mark was going to check to see if a service could have
>   Simon> more than one service ontology term attached to it, I think
>   Simon> he said they could. Using OWL and reasoning would allow
>   Simon> services to be described by their properties (input/output,
>   Simon> what the service does, etc.) and the reasoning process would
>   Simon> slot services into all the correct places that they belong,
>   Simon> based on their properties - this would alleviate the problem
>   Simon> of trying to fit a service into one service ontology
>   Simon> category.
>
>
> As it stands I think you could do this without reasoning. Essentially
> what you are asking for here is a multiple inheritance tree, I
> think. Where OWL gets very powerful is if your properties are
> complex, have constraints on them, or there are lots of them.
>
>
>   Simon> [This would be more S-MOBY-esque, the RDF for the service
>   Simon> could describe its properties and the discovery engine
>   Simon> (moby-google, moogle?) could use those properties to slot it
>   Simon> into the service ontology strucutre appropriately, no
>   Simon> registration, etc required]
>
>
>   Simon> I divided into bioApplicationService and
>   Simon> infrastructureService as children of the parent ServiceClass
>   Simon> node to try and separate bioinformatics services from other
>   Simon> types of service that arent really bioinformatics but are
>   Simon> essential to the system - service registration, etc. What are
>   Simon> other's thoughts on this? I noticed I left Resolution in the
>   Simon> wrong branch.
>
>
>   Simon> At this point, have a look at what I have and give me your
>   Simon> input and I'll go from there. I will also try and assemble a
>   Simon> bibliography of all the papers I've been reading on OWL,
>   Simon> etc., they would be useful for understanding S-MOBY too I
>   Simon> suspect.
>
>
> I will try and comment on what you have in the next few days.
>
> Cheers
>
> Phil
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>
>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw