Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Slow system response

Paul R Alexander palexander at stanford.edu
Wed Aug 1 17:56:50 PDT 2012


Cassandra,

Thanks for the data points here. When I checked the links you provide 
they were all working, which isn't surprising. The BioPortal web site 
caches many REST calls, so when you first attempted to visit the pages 
my guess is that the calls got cached and were relatively fast after that.

I have one question: did you see problems with all of the ontologies in 
your test cases? Or just the ones you list below? If you had successful 
tests, can you let me know which ontologies were successful?

We did see an increase in traffic at 3:00pm PST due to bots indexing the 
site. This may have had something to do with the slowness you 
experienced, but we generally absorb these increases in traffic without 
too much problem.

One of the things we are working on is implementing a suite of testing 
and monitoring tools that give us information about a wide variety of 
terms in BioPortal. Currently we monitor a small number of term pages, 
both on the UI and REST side. However, using the same terms over and 
over in monitoring doesn't give us great data about what happens when 
someone first visits a term page that isn't currently in the cache.

We're also testing some alternative ways to store the information for 
UMLS ontologies (all of the ontologies you list below are UMLS), which 
may provide some improvements.

Please let me know if you have other questions related to this. We'll 
try to keep people abreast of improvements in speed and reliability as 
we make them.

Paul


On 8/1/12 3:35 PM, Cassandra Petrachenko wrote:
> Hi Support:
>
> I'm experiencing slow response times when browsing terms in BioPortal. 
> This was occurring when I starting working with BioPortal at ~ 3:05 PST
>
> For example, these Full Id URLs also took a few minutes to load:
> http://purl.bioontology.org/ontology/NDFRT/N0000000030
> http://purl.bioontology.org/ontology/SNOMEDCT/105590001
> http://purl.bioontology.org/ontology/NDFRT/N0000181236 - this one just 
> resolved with "We're sorry but something has gone wrong..."
>
> I'm also going through portions of my visualization test cases from 
> last week and I'm not able to view a variety of terms in our UAT BioMixer:
>
> /1352 National Drug File/
>
>   * Female Urogenital Diseases [Disease/Finding]:
>     http://purl.bioontology.org/ontology/NDFRT/N0000181236 Constructed
>     URL:
>     http://20120719-1.bio-mixer.appspot.com/?mode=embed&embed_mode=paths_to_root&virtual_ontology_id=1352&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNDFRT%2FN0000181236&userapikey=
>
>   * Metabolic Diseases [Disease/Finding]:
>     http://purl.bioontology.org/ontology/NDFRT/N0000002004 Constructed
>     URL:
>     http://20120719-1.bio-mixer.appspot.com/?mode=embed&embed_mode=paths_to_root&virtual_ontology_id=1352&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNDFRT%2FN0000002004&userapikey=
>
>   * Liquid [Dose Form]:
>     http://purl.bioontology.org/ontology/NDFRT/N0000135726 Constructed
>     URL:
>     http://20120719-1.bio-mixer.appspot.com/?mode=embed&embed_mode=paths_to_root&virtual_ontology_id=1352&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNDFRT%2FN0000135726&userapikey=
>
>
> /1353 SNOMED Clinical Terms/
>
>   * Mechanical stress:
>     http://purl.bioontology.org/ontology/SNOMEDCT/285655001
>     Constructed URL:
>     http://20120719-1.bio-mixer.appspot.com/?mode=embed&embed_mode=paths_to_root&virtual_ontology_id=1353&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F285655001&userapikey=
>
>
> /1422 MedDRA/
>
>   * Blood and lymphatic system disorders:
>     http://purl.bioontology.org/ontology/MDR/10005329 Constructed URL:
>     http://20120719-1.bio-mixer.appspot.com/?mode=embed&embed_mode=paths_to_root&virtual_ontology_id=1422&full_concept_id=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMDR%2F10005329&userapikey=
>
>
>
>
>
> Is there anything happening on the BioPortal side that could be 
> causing this? Could this be network issues on my side? (Though I'm not 
> experiencing delays with other websites.)
>
>
>
>
> Regards,
>
> Cassandra L. Petrachenko
> /Research Associate
> The CHISEL Group, University of Victoria
> http://www.thechiselgroup.org
> 250-472-5775/
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20120801/01925ad6/attachment-0001.html>


More information about the bioontology-support mailing list