Peter et al:
The latest COSMO, (r877) which was tested in several utilities, was
uploaded a few days ago and hasn’t yet reached the "Parsing Ontology" phase.
Is there any way to force a parse? (01)
Pat (02)
Patrick Cassidy
MICRA, Inc.
908-561-3416
cell: 908-565-4053
cassidy@xxxxxxxxx (03)
> -----Original Message-----
> From: oor-dev-bounces@xxxxxxxxxxxxxxxx [mailto:oor-dev-
> bounces@xxxxxxxxxxxxxxxx] On Behalf Of Natasha Noy
> Sent: Wednesday, February 17, 2010 2:22 PM
> To: OpenOntologyRepository-development
> Subject: Re: [oor-dev] Parsing Ontologies [was - Fwd: registration...
> oor sandbox (v2.x)]
>
> A good test is usually to see if the ontology opens up fine in Protege
> 3.4. That's the version of Protege that BioPortal uses. If Protege
> can't handle it, BioPortal won't be able to do it either.
>
> Natasha
>
>
> On Feb 17, 2010, at 11:15 AM, Patrick Cassidy wrote:
>
> > Paul,
> > Thanks for looking into this. The COSMO has over 7000 classes,
> > over 700
> > relations and about 1600 restrictions, and is multi-inheritance. So
> > it is
> > more complex than many domain or utility ontologies. It also uses
> > rdfs:class as well as owl:class, which seems to confuse at least one
> > version
> > of Protégé (though not others!).
> > If the parser throws off some error message I'd like to see it.
> >
> > Pat
> >
> > Patrick Cassidy
> > MICRA, Inc.
> > 908-561-3416
> > cell: 908-565-4053
> > cassidy@xxxxxxxxx
> >
> >
> >> -----Original Message-----
> >> From: Paul R Alexander [mailto:palexander@xxxxxxxxxxxx]
> >> Sent: Wednesday, February 17, 2010 12:56 PM
> >> To: Peter Yim
> >> Cc: OpenOntologyRepository-development; Patrick Cassidy; Tejas
> Parikh
> >> Subject: Re: Parsing Ontologies [was - Fwd: registration... oor
> >> sandbox
> >> (v2.x)]
> >>
> >> Peter,
> >>
> >> It sounds like there was a failure at some point during the ontology
> >> parsing process, meaning that the process had started, setting the
> >> ontology status to "Parsing", but never finished, so the ontology
> >> status
> >> was never updated. There is a "Parsing Error" status, I'm not sure
> >> why
> >> that wasn't set if a problem was encountered. I would try to login
> to
> >> the BioPortal Admin software and trigger a re-parse on Pat's
> >> ontology.
> >> If it does encounter an error during the process, the Admin UI
> should
> >> report that back to you.
> >>
> >> Paul
> >>
> >> On 2/17/10 8:41 AM, Peter Yim wrote:
> >>> Paul or Someone from NCBO who might point us in the right
> >> direction ...
> >>>
> >>> Further to the earlier exchange with PatCassidy (below), looks like
> >>> his COSMO ontology (which Pat uploaded on 2010.02.11) is still
> >>> "being
> >>> parsed" at the OOR-Sandbox (v2.x).
> >>>
> >>> (Not knowing what exactly to look for) I just went into the server
> >> and
> >>> check cpu workload on the<oor-01> vm. To my surprise, the cpu(s)
> is
> >>> running at 99.5% to 100% idle. ... I do notice that 19 (of the 116)
> >>> ontologies that are listed in the "Browse" page are supposed to be
> >>> in
> >>> the state of "Parse Ontology." ... therefore, this doesn't sound
> >>> right!
> >>>
> >>> ... Suggestions?
> >>>
> >>> Thanks& regards. =ppy
> >>> --
> >>>
> >>>
> >>> ---------- Forwarded message ----------
> >>> From: Patrick Cassidy<pat@xxxxxxxxx>
> >>> Date: Fri, Feb 12, 2010 at 7:31 PM
> >>> Subject: RE: registration problem oor sandbox (v2.x)
> >>> To: Peter Yim<peter.yim@xxxxxxxx>
> >>> Cc: Tejas Parikh<tejas@xxxxxxxxxxxxxxx>, Paul R Alexander
> >>> <palexander@xxxxxxxxxxxx>, Ken Baclawski<kenb@xxxxxxxxxxx>, "Obrst,
> >>> Leo J."<lobrst@xxxxxxxxx>, Mike Dean<mdean@xxxxxxx>
> >>>
> >>>
> >>> On the parsing time for the new sandbox:
> >>>
> >>>>
> >>>>> [PatC] Any idea how long a 7000 element ontology should take to
> >>>>>
> >>>> parse?
> >>>>
> >>>> [ppy] (I'm guessing, but) I don't think anyone knows* ... Please
> >> make
> >>>> a note on how long it is taking this time for COSMO, maybe when
> you
> >>>> are done, you can share the experience with all of us. [ *since
> >>>> different installs are running on fairly different hardware and
> >>>> platforms, and experiencing different work loads all the time. ]
> >>>>
> >>> The COSMO is still "parsing" after over 24 hours. I see a parsing
> >> error for
> >>> the OWL-time ontology (didn't see that in the last version). Who
> is
> >>> maintaining the parser and display function? Any thoughts on how
> >> this can
> >>> be improved?
> >>>
> >>> The "explore" function is really valuable. I hope we can get it to
> >> be
> >>> consistently effective. Sorry I have no programming expertise to
> >> help out
> >>> here.
> >>>
> >>> Pat
> >>>
> >>> Patrick Cassidy
> >>> MICRA, Inc.
> >>> 908-561-3416
> >>> cell: 908-565-4053
> >>> cassidy@xxxxxxxxx
> >>>
> >
> >
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