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[bioontology-support] Apologies

Natasha Noy noy at stanford.edu
Mon Aug 31 12:24:09 PDT 2009


Hi Eamonn,

Have you tried this one:
http://www.berkeleybop.org/obo-conv.cgi

It's supposed to do the job but we haven't tested it on our side. It  
is on our to do list though. Let us know if you do try it and it works  
for you.

Natasha


On Aug 28, 2009, at 11:08 AM, maguire at ebi.ac.uk wrote:

> I'm not sure. I'd say not many people would need it :o) do you guys  
> happen
> to know of an api I can use to convert obo to owl? I tried oboedit  
> but the
> api (I use the term lightly!) doesn't give much insight about how to  
> use
> it! Plus, I tried to get in contact with the author of the paper but
> he/she never replied!
>
> Thanks,
> Eamonn
>
>> Would also including the inferred version of the ontologies, OWL,  
>> OBO(?)
>> on
>> BioPortal for download be preferred?
>>
>>
>>
>> Trish
>>
>>
>>
>>
>>
>> From: Eamonn Maguire [mailto:maguire at ebi.ac.uk]
>> Sent: Friday, August 28, 2009 7:49 AM
>> To: Trish Whetzel
>> Cc: bioontology-support at mailman.stanford.edu
>> Subject: Re: [bioontology-support] Apologies
>>
>>
>>
>> Only the OWL ontologies, and it was in parallel. I have created a  
>> service
>> with a pool of 4 threads to do this as quickly as possible, but i  
>> didn't
>> expect that to happen since i wasn't performing any real queries,  
>> just
>> fetching ontology files.
>>
>>
>>
>> The latency being experienced was a result of the time it takes to
>> classify
>> an ontology using the Pellet reasoner, not anything to do with  
>> bioportal.
>> I
>> have to do this to build the ontology tree for viewing within the
>> configuration tool. You will see what this looks like when i send the
>> use-case doc later on! Through using my service, i can run it whilst
>> packaging up the configuration tool so that the majority of  
>> ontologies
>> will
>> be available for browsing instantly rather than having to wait for
>> ontologies such as OBI to get classified (since the large number of  
>> axioms
>> cause the reasoner to either run out of memory or take an extremely  
>> long
>> time).
>>
>>
>>
>> thanks
>>
>>
>>
>> Eamonn
>>
>>
>>
>>
>>
>> On 28 Aug 2009, at 15:41, Trish Whetzel wrote:
>>
>>
>>
>>
>>
>> It seems fine now.
>>
>>
>>
>> How many ontologies were you trying to download  and was that in  
>> parallel?
>> Also, without downloading the ontology what latency were you  
>> experiencing?
>>
>>
>>
>> Trish
>>
>>
>>
>>
>>
>> On Aug 28, 2009, at 3:54 AM, Eamonn Maguire wrote:
>>
>>
>>
>>
>>
>> Hi all,
>>
>>
>>
>> your server is now not responding and i think this may be  
>> inadvertedly
>> down
>> to me! I have a service which has a number of threads running to  
>> download
>> ontologies from bioportal and then reason over them to build ontology
>> trees
>> so that the user experiences no latency when browsing ontologies  
>> inside
>> the
>> configurator. Unfortunately, i don't think your server was up to such
>> requests so Bioportal now seems to be down.
>>
>>
>>
>> I sincerely apologise, but i didn't expect this to happen since i'm  
>> only
>> requesting ontology files for download, not doing any queries per se!
>>
>>
>>
>> eamonn
>>
>>
>>
>> --
>>
>> *          maguire at ebi.ac.uk
>>
>> :           http://www.ebi.ac.uk/~maguire
>>
>> :     http://www.ebi.ac.uk/net-project
>>
>>
>>
>>
>>
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>>
>>
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>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>>
>>
>> --
>>
>> *          maguire at ebi.ac.uk
>>
>> :           http://www.ebi.ac.uk/~maguire
>>
>> :     http://www.ebi.ac.uk/net-project
>>
>>
>>
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>
>
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