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[bioontology-support] Apologies

Trish Whetzel whetzel at stanford.edu
Fri Aug 28 10:28:58 PDT 2009


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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--

*          maguire at ebi.ac.uk

:           http://www.ebi.ac.uk/~maguire

:     http://www.ebi.ac.uk/net-project

 

 

 

 

 

 

 

 

 

 

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