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[bioontology-support] [BioPortal] Feedback from Pei

Paul R Alexander palexander at stanford.edu
Fri Oct 3 11:43:09 PDT 2014


I cannot reproduce this behavior either. The given page returns result appropriately for me.

One thing I noticed is that you are requesting children for each class. If you are traversing the entire ontology and wanting to build the hierarchy, you are better off just getting the parents. SNOMED has some concepts which have tens of thousands of children and it could cause issues in response times.

Paul


On Oct 3, 2014, at 11:32 AM, Chen, Pei <Pei.Chen at childrens.harvard.edu> wrote:

> I think I narrowed that what was causing the issue for me..
> Do you know why some pages seem to return a <nilClass> instead of <class>  Is this expected?
> 
> 
> 
> Check out the response from this request as an example:
> http://data.bioontology.org/ontologies/SNOMEDCT/classes?include=properties,synonym,children&format=xml&apikey=[REDACTED] &page=254
> 
> Other pages will return <class> as the root element.  But that one returned <nilClass> as root.
> It seems pretty consistent:
>  <?xml version="1.0" encoding="UTF-8" ?> 
> <- <nilClass>
> <  <page>254</page> 
> <  <pageCount>6011</pageCount> 
> <  <prevPage>253</prevPage> 
> <  <nextPage>255</nextPage> 
> <- <links>
> <  <nextPage>http://data.bioontology.org/ontologies/SNOMEDCT/classes?include=properties%2Csynonym%2Cchildren&format=xml&apikey=8583c5c0-94af-4677-aa6e-77277049e212&page=255</nextPage> 
> <  <prevPage>http://data.bioontology.org/ontologies/SNOMEDCT/classes?include=properties%2Csynonym%2Cchildren&format=xml&apikey=8583c5c0-94af-4677-aa6e-77277049e212&page=253</prevPage> 
>  </links>
>  <<collection /> 
>  </nilClass>
> 
>> -----Original Message-----
>> From: Paul R Alexander [mailto:palexander at stanford.edu]
>> Sent: Thursday, October 02, 2014 7:08 PM
>> To: support at bioontology.org
>> Cc: Chen, Pei
>> Subject: Re: [bioontology-support] [BioPortal] Feedback from Pei
>> 
>> I cannot reproduce this. Could you try again and let me know if it is still
>> broken for you?
>> 
>> Thanks,
>> Paul
>> 
>> 
>> On Oct 2, 2014, at 1:26 PM, support at bioontology.org wrote:
>> 
>>> 
>>> Name: Pei
>>> 
>>> Email: pei.chen at childrens.harvard.edu
>>> 
>>> Location:
>> http://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&concep
>> tid=http://purl.bioontology.org/ontology/SNOMEDCT/70819003&jump_to_n
>> av=true
>>> 
>>> Comment:
>>> Hi,
>>> Do you know why page 1102 for this request returns an Internal Server
>> Error?  Other pages such as 1101 or 1103 work fine...
>>> 
>>> 
>> http://data.bioontology.org/ontologies/SNOMEDCT/classes?include=proper
>> ties,synonym,children&format=xml&apikey=[REDACTED]&page=1102
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
> 




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