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[bioontology-support] [BioPortal] Feedback from Maxwell Neal

Maxwell Neal maxneal at gmail.com
Fri May 20 10:08:04 PDT 2016


Thanks Michael!
I've confirmed that I can now retrieve that term on my end.
Cheers,

M

On Wed, May 18, 2016 at 5:49 PM, Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Maxwell,
>
> This should be resolved now. It looks like GO hasn't been indexed for a
> while, and the version we have in our search index is not the latest
> submission of the ontology. I've done some more granular troubleshooting of
> indexing this specific term:
>
> http://purl.obolibrary.org/obo/GO_0005891 (voltage-gated calcium channel
> complex)
>
> There is absolutely nothing abnormal about it. It indexes just fine in my
> local environment. Please let me know if you continue experiencing issues
> with this or see any other abnormalities with our search.
>
> Thank you,
>
> Michael
>
>
> On May 11, 2016, at 12:16, Maxwell Neal <maxneal at gmail.com> wrote:
>
> OK Michael thanks very much for the update!
>
> M
>
> On Wed, May 11, 2016 at 3:00 PM, Michael Dorf <mdorf at stanford.edu> wrote:
>
>> Hi Maxwell,
>>
>> Thank you for bringing this to our attention. At this point, I don't have
>> a definitive answer for you other than "it should work, but it doesn't".
>> :-) One thing I did verify is that the term IS missing from our search
>> index. Troubleshooting this further isn't trivial as it requires a
>> "controlled" re-indexing of the ontology to see whether this term gets
>> skipped, errors out, or simply returns empty data.
>>
>> I'll have to get back to you oaths, hopefully within days.
>>
>> Thank you for your patience!
>>
>> Michael
>>
>>
>> On May 10, 2016, at 08:05, support at bioontology.org wrote:
>>
>> Name: Maxwell Neal
>>
>> Email: mneal at uw.edu
>>
>> Location:
>> http://bioportal.bioontology.org/ontologies/GO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0005891
>>
>>
>> *Feedback:*
>>
>> Hello,
>>
>> I'm having trouble retrieving the GO term "voltage-gated calcium channel
>> complex" (GO_0005891) using the BioPortal REST services. When I use the
>> following call, no results are returned:
>>
>>
>> http://data.bioontology.org/search?q=voltage-gated+calcium+channel+complex&ontologies=GO&format=xml&exact_match=true&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a
>>
>> Also, a broader search on "calcium" does not return the term:
>>
>>
>> http://data.bioontology.org/search?q=channel&ontologies=GO&format=xml&exact_match=false&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a
>>
>> Any help is appreciated!
>>
>> - Max
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>
>
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