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. (02)
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
Anyway, I thought this info might be helpful. (04)
> -----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)]
> 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
> If it does encounter an error during the process, the Admin UI should
> report that back to you.
> 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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