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[bioontology-support] Apologies

maguire at ebi.ac.uk maguire at ebi.ac.uk
Fri Aug 28 11:08:55 PDT 2009


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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> 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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