[MOBY-dev] Quick poll

Tue Apr 11 14:11:59 UTC 2006

Hi Paul,

I will update the parsers in a moment and let you know. We made some changes
yesterday to the RDF to make our ontologies owl-dl (actually Mark is trying to
make owl-dl and I just code the changes ;-).

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org 
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon
> Sent: Tuesday, April 11, 2006 7:10 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Quick poll
> 
> It is in the Object ontology, but only the last two lines I 
> guess, which look like:
> 
> <owl:AnnotationProperty
> rdf:about="http://www.w3.org/2000/01/rdf-schema#comment">
> 
> In the file 
> http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects
> 
> Which causes the following error (so the problem might 
> actually be that org.biomoby.shared.extended.DataTypeParser 
> should ignore this field but
> doesn't?):
> 
> Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: 
> Expected an LSID as a URI, instead got
> http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the
> form: 
> urn:lsid:<AuthorityID>:<NamespaceID>:<ObjectID>:[RevisionID], got: 
> urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment]
> 
> org.biomoby.shared.MobyException: Expected an LSID as a URI, 
> instead got http://www.w3.org/2000/01/rdf-schema#comment 200 
> : LSID must be of the
> form: 
> urn:lsid:<AuthorityID>:<NamespaceID>:<ObjectID>:[RevisionID], got: 
> urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment]
> 
>    at
> org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFro
> mRDF(DataTypeParser.java:173)
> 
> > Hi Paul,
> >
> > Can you send us a copy of what you are seeing, and the URL that you 
> > retrieved it from?  From our perspective, it is still LSID-based...
> >
> > ??
> >
> > M
> >
> >
> > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon 
> <gordonp at ucalgary.ca>
> > wrote:
> >
> >   
> >> Umm.. the test server has reverted to 
> >> http://www.w3.org/2000/01/rdf-schema#label  type RDF 
> instead of LSID 
> >> based.  Is this intentional?  It breaks all my code :-(
> >>     
> >>> Hi,
> >>>
> >>> The agent isnt on yet (on mobycentral that is, it is 
> running on the 
> >>> test registry). We want to make sure that the RDF is 100% correct 
> >>> before the agent is deployed.
> >>>
> >>> Thanks,
> >>>
> >>> Eddie
> >>>
> >>>
> >>>       
> >>>> -----Original Message-----
> >>>> From: moby-dev-bounces at lists.open-bio.org
> >>>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Arnaud 
> >>>> Kerhornou
> >>>> Sent: Friday, April 07, 2006 2:04 AM
> >>>> To: Core developer announcements
> >>>> Subject: Re: [MOBY-dev] Quick poll
> >>>>
> >>>> Hi Eddie,
> >>>>
> >>>> I have updated my services, and they all have a signature URL. I 
> >>>> have a RDF document that includes in it all my services 
> in there, 
> >>>> http://genome.imim.es/webservices/RDFs/services.rdf
> >>>>
> >>>> i don't use the RDF, i guess in future i could use it for 
> >>>> parameters and input objects validation - this way 
> validatino could 
> >>>> be done on the fly generically.
> >>>>
> >>>> Also, quick question, is the agent on ? Is it going to check the 
> >>>> RDF document on a regular basis, and being able to update the 
> >>>> central registry if i modify the specs of my services?
> >>>>
> >>>> regards,
> >>>> Arnaud
> >>>>
> >>>> Edward Kawas wrote:
> >>>>
> >>>>         
> >>>>> Hi,
> >>>>>
> >>>>> Just out of curiosity, who is using the RDFs that 
> mobycentral is 
> >>>>> currently generating. If you are using them, what tasks are
> >>>>>
> >>>>>           
> >>>> you using them for.
> >>>>
> >>>>         
> >>>>> I ask, because the RDF that is generated by mobycentral is
> >>>>>
> >>>>>           
> >>>> different
> >>>>
> >>>>         
> >>>>> than the one that is generated by the test machine. The 
> difference 
> >>>>> lies on the fact that mobycentral identifies resources
> >>>>>
> >>>>>           
> >>>> based on URIs,
> >>>>
> >>>>         
> >>>>> while the test registry uses LSIDs. There are some other
> >>>>>
> >>>>>           
> >>>> changes, but
> >>>>
> >>>>         
> >>>>> mainly additions (for instance, object ontology rdf now 
> has more 
> >>>>> information in it, like the authority of the creator, the
> >>>>>
> >>>>>           
> >>>> creators email address, etc).
> >>>>
> >>>>         
> >>>>> We are hoping to deploy the new RDF onto mobycentral very
> >>>>>
> >>>>>           
> >>>> soon, and I
> >>>>
> >>>>         
> >>>>> just want to get a head count of who it is that will yell (beat 
> >>>>> up,
> >>>>> etc) at me ;-)
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> Eddie
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>           
> >>>> _______________________________________________
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> >>>> MOBY-dev at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>>>
> >>>>         
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> >>>
> >>>       
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> >>     
> >
> >
> >
> >   
> 
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