Peter, (01)
> One thing though .. you said " the process [of the
> "bioportal_admin" re-parsing of COSMO ontology] did complete (02)
Sorry I wasn't more clear... I was using our BBN OOR instance, after the
COSMO ontology got federated (copied) there from the CIM3 sandbox. (03)
Jim (04)
> -----Original Message-----
> From: Peter Yim [mailto:peter.yim@xxxxxxxx]
> Sent: Wednesday, February 17, 2010 8:41 AM
> To: jchatign@xxxxxxx; Paul R Alexander
> Cc: OpenOntologyRepository-development
> Subject: Re: [oor-dev] Parsing Ontologies [was - Fwd:
> registration... oorsandbox (v2.x)]
>
>
> Thanks, Jim ... allow me to defer to the NCBO folks to make
> sense out of this, and provide us pointers on what to do next
> (given your
> input.)
>
> One thing though .. you said " the process [of the
> "bioportal_admin" re-parsing of COSMO ontology] did complete
> in a about 2 hours despite the "exception" ... I still see
> that it shows the state of "Parse Ontology" on the
> OOR-sandbox "Browse" screen, and I don't see that this COSMO
> ontology can be "explore(d)" yet.
>
> Thanks & regards. =ppy
> --
>
>
> On Wed, Feb 17, 2010 at 10:20 AM, <jchatign@xxxxxxx> wrote:
> > Peter,
> >
> > As I was putting my slides together for Friday's telcon, I
> happened to
> > pick the COSMO ontology for use with a screen shot. I wanted the
> > "visualize" link to be active, so I used bioportal_admin to
> parse it.
> >
> > Attached is the relevant messages from the log file. (And a
> portion of
> > a screen shot). There was a Java exception raised during
> the parsing,
> > but the process did complete in a about 2 hours. Perhaps when the
> > parser was invoked on the OOR sandbox as a scheduled (cron)
> job, the
> > exception cause it to abort?
> >
> > Anyway, I thought this info might be helpful.
> >
> > Jim
>
>
> >> -----Original Message-----
> >> From: Paul R Alexander [mailto:palexander@xxxxxxxxxxxx]
> >> Sent: Wednesday, February 17, 2010 7:56 AM
> >> To: Peter Yim
> >> Cc: OpenOntologyRepository-development
> >> Subject: Re: [oor-dev] Parsing Ontologies [was - Fwd:
> registration...
> >> oorsandbox (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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> >>
> >
> (05)
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