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[bioontology-support] Bioportal NCIT Import problem

Trish Whetzel whetzel at stanford.edu
Tue Apr 27 16:50:03 PDT 2010


Hi Girish,

That is really good news to hear that the import speed is improved  
using the getAllTerms Web service. In the case for NCIt, we recently  
found that there is a duplicate listing (based on NCIt also now being  
listed on the OBO Foundry web page) and I will remove this duplicate  
entry. In addition, we will also have some improved QA to more quickly  
check for this case.

However, there is also a version of the NCIt with version identifier  
'42693' that is local to BioPortal and therefore the following call  
works: http://rest.bioontology.org/bioportal/concepts/42693/all?pagesize=1000&pagenum=1&email=kevin.jude.mitchell@gmail.com

One thing that you can do to prevent trying to call a 'remote'  
ontology is if you are using the call:
http://rest.bioontology.org/bioportal/ontologies?email=example@example.org 
  to get a list of the ontologies, parse our the <statusId> field and  
display only those that have the value '3', which means that the  
ontology is local to BioPortal.  If you don't use this call, perhaps  
we can explore adding a more meaningful error message in the output of  
the getAllTerms web service.

Trish


On Apr 27, 2010, at 3:52 PM, Chavan, Girish wrote:

> Hi All,
>
> We have our new import code almost ready. We tested it with GO, FMA  
> and Radlex, and the import speed is very fast. We have having an  
> error downloading from NCIT though.
>
> Here is the service call and error:
>
> Server returned HTTP response code: 500 for URL:
> http://rest.bioontology.org/bioportal/concepts/42697/all?pagesize=1000&pagenum=1&email=kevin.jude.mitchell@gmail.com
>
>
> Could you shed some light as to what might be going on?
>
> Thanks,
> Girish
>
>

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