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. (01)
Natasha (02)
On Feb 17, 2010, at 11:15 AM, Patrick Cassidy wrote: (03)
> 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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