Dear All,

as next Monday's SWDT agenda contains "Ontology Service Specifications &
Development - feedback and discussion", and Barry asked us to organize
the feedback, it would be great if people could give some feedback
either here on the mailing list (as Nina already did), or in a direct
mail to Andreas Karwath or me. 
The slides from last Monday's meeting can be found here:
http://www.opentox.org/data/documents/development/framework-design/ontology-service/view

best regards,
Tobias

On Mon, 2010-11-08 at 10:09 +0100, Tobias Girschick wrote: 
> On Mon, 2010-11-08 at 10:59 +0200, Nina Jeliazkova wrote:
> > Hi Tobias, Andreas,
> > 
> > Many thanks!  
> > 
> > Please find my thoughts on this topic below.
> > 
> > Slide 2: What resources to register
> > 
> > Register: Algorithms and models, reports, validation, Dataset metadata
> > and feature representations , no feature values, no compounds.
> > 
> > Slide 3: Deregistering
> > 
> > Several approaches:
> > 1)Services register/deregister themselves .  Crash and servers
> > disapearing can only be solved via timeouts / life span of a
> > registration .   Using keepalives complicates the protocol in many
> > ways.
> > 2)Services don‘t register themselves, the ontology server(s) which are
> > querying and gathering information (similar as a search engine – there
> > are bots that gather information, not web servers registering into
> > Google data centers)
> > 3)Some compromise between the two (e.g. Services register once , the
> > ontology server acts like a bot and refreshes the info periodically)
> 
> I like that idea (3). 
> 
> > 
> > 
> > Slide 4: Duplicate registration
> > 
> > If URIs are unique, there is no problem, the underlying RDF storage
> > will recognize duplicates.
> > 
> > There is a problem with anonymous resources in RDF though.  I would
> > suggest avoiding anonymous resources as much as possible.
> > 
> > 
> > Slide 5:  Scenario: all necessary resources registered, but not all
> > public:
> > 
> > We need a representation of users and their access rights in
> > opentox.owl . There is no RDF representation of users in opentox.owl
> > so far.
> > 
> > LDAP  groups will need some RDF representation as well (perhaps there
> > is an existing ontology?) .  Some RDF storages have support for user
> > accounts and offer some levels of security.
> > 
> > In order to register a resource, the ontology server connects to the
> > resource and reads its RDF representation.  If the resource is
> > protected, the ontology server will not be able to read the RDF,
> > unless it has rights to do so.  How do we handle this situation?
> > 
> > As the ontology will publish metadata only (no compounds, no feature
> > values) there is not much danger in exposing sensitive resources.
> > 
> > 
> > Slide 6: Quality of resources (how to test for compliance)
> > 
> > Compliance – there should be computer readable specification (wadl,
> > owl, etc.) , which enables to check any OT service against it. 
> 
> I agree. 
> 
> > I have an initial draft of opentox-rest.owl, which aims at
> > representing the spec (REST operations) as an ontology, additional to
> > opentox.owl, which represents the resources themselves.
> > Will publish it shortly into Collaborative Protege.
> > 
> > Approval by named experts – (again) we would need RDF representation
> > of users (can use FOAF) and assign status of „Expert“ to some of them
> > (how, when, who will say who is an expert?)
> 
> Well, that is hard to say. I guess, at least in the beginning, we would
> have to do that. But the very important fact is that the name of the
> expert appears (and maybe some short profile or link). 
> 
> Best regards,
> Tobias
> 
> > 
> > Best regards,
> > Nina
> > 
> > 
> > 
> > 
> > 
> > On 8 November 2010 10:04, Tobias Girschick
> > <tobias.girschick at in.tum.de> wrote:
> >         Hi All,
> >         
> >         as promised in last weeks meeting, I uploaded the notes
> >         Andreas K. and I
> >         took during our brainstorming session on the ontology service:
> >         
> >         http://www.opentox.org/data/documents/development/framework-design/ontology-service/view
> >         
> >         Andreas, please feel free to add anything I forgot.
> >         
> >         best regards,
> >         Tobias
> >         
> >         --
> >         Dipl.-Bioinf. Tobias Girschick
> >         
> >         Technische Universität München
> >         Institut für Informatik
> >         Lehrstuhl I12 - Bioinformatik
> >         Bolzmannstr. 3
> >         85748 Garching b. München, Germany
> >         
> >         Room: MI 01.09.042
> >         Phone: +49 (89) 289-18002
> >         Email: tobias.girschick at in.tum.de
> >         Web: http://wwwkramer.in.tum.de/girschick
> >         
> >         _______________________________________________
> >         Development mailing list
> >         Development at opentox.org
> >         http://www.opentox.org/mailman/listinfo/development 
> > 
> 

-- 
Dipl.-Bioinf. Tobias Girschick

Technische Universität München
Institut für Informatik
Lehrstuhl I12 - Bioinformatik
Bolzmannstr. 3
85748 Garching b. München, Germany

Room: MI 01.09.042
Phone: +49 (89) 289-18002
Email: tobias.girschick at in.tum.de
Web: http://wwwkramer.in.tum.de/girschick