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 Prot�g� (though not others!).
If the parser throws off some error message I'd like to see it. (01)
Pat (02)
Patrick Cassidy
MICRA, Inc.
908-561-3416
cell: 908-565-4053
cassidy@xxxxxxxxx (03)
> -----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
> > (04)
_________________________________________________________________
Message Archives: http://ontolog.cim3.net/forum/oor-dev/
Config/Unsubscribe: http://ontolog.cim3.net/mailman/listinfo/oor-dev/
Shared Files: http://ontolog.cim3.net/file/work/OOR/dev/
Wiki: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository (05)
|