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[bioontology-support] [BioPortal] Feedback from Phil Kiossoglou

Phil Kiossoglou phil.kiossoglou at gmail.com
Sat May 5 20:08:31 PDT 2018


Can confirm it's working on my end.

Thanks for all the help,

Phil

On 27 April 2018 at 09:28, Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Phil,
>
> Just FYI, this problem has been fixed. Let me know if you experience
> further issues.
>
> Thanks,
>
> Michael
>
>
> On Apr 17, 2018, at 4:11 PM, Michael Dorf <mdorf at stanford.edu> wrote:
>
> Just FYI, the issue is tracked here:
>
> https://github.com/ncbo/ncbo_ontology_recommender/issues/7
>
> Michael
>
> On Apr 17, 2018, at 3:22 PM, Michael Dorf <mdorf at stanford.edu> wrote:
>
> Hi Phil,
>
> Thanks for keeping in touch. This definitely appears to be a bug in our
> system. There is no reason for the Recommender to blow up when given the
> word “concept” (or any input for that matter). I am still hunting for the
> root cause. The fix will most likely require a code release. I’ll keep you
> posted when I have more details.
>
> Thanks!
>
> Michael
>
>
> On Apr 15, 2018, at 7:35 PM, Phil Kiossoglou <phil.kiossoglou at gmail.com>
> wrote:
>
> Hi John,
>
> Thanks for the insight.  Just ran again and still getting the error
> (related to the term "concept", deleting it manages to make it work in this
> particular instance).
>
> Just wondering if there's anything I can contribute to help with a fix?
> (I'm aware the answer to this is probably "not really").
>
> Thanks and regards,
>
> Phil
>
>
> On 18 March 2018 at 03:41, John Graybeal <jgraybeal at stanford.edu> wrote:
>
>> Phil, thank you for sending your issue, sorry it was a pain for so long.
>>
>> After some trial and error, I found the problem word in your text is
>> 'concept'. Delete that word and you can have recommendations for the rest
>> of this text.
>>
>> As a more permanent fix, we'll have to look in the index to see what has
>> been corrupted. I think this will be straightforward, but it may be a few
>> days before we can get to it. We'll send an email once fixed.
>>
>> john
>>
>> On Mar 16, 2018, at 11:42 PM, support at bioontology.org wrote:
>>
>> Name: Phil Kiossoglou
>>
>> Email: phil.kiossoglou at gmail.com
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org
>> <http://2fbioportal.bioontology.org/>%2Frecommender
>>
>>
>> *Feedback:*
>>
>> Attempting to use the NCBO recommender, both via the API and via the
>> online web app is generating errors. In the case of the API, these are HTTP
>> 500 errors.
>>
>> This issue has been persisting for > 1 week.
>>
>> The text I am supplying is (without quotes):
>>
>> "Inflammatory bowel disease (IBD) including Crohn's disease (CD) and
>> ulcerative colitis (UC), is an immunologically mediated chronic disease.
>> The key underlying pathology is a deregulated immune response to commensal
>> flora in a genetically susceptible host. Advances in genomics, epigenomics
>> and understanding of the microbiome have brought forth the role of these
>> spheres in the pathogenesis of IBD. Yet these factors explain only a small
>> fraction of disease risk and our ability to predict relapses and response
>> to treatment remains dismal. The external environment plays an important
>> role in modifying the risk of IBD and in precipitating relapses in patients
>> with established disease. The term 'exposome' was proposed to reflect a
>> life-course of environmental influences beginning in-utero and proceeding
>> right through childhood to adulthood. While the exposome is still a concept
>> which needs practical perspective to enable better patient care, this
>> review examines the gaps in our understanding that the IBD exposome helps
>> explain. We further highlight the definition and parameters of this metric
>> which can be incorporated for its application in research and clinical
>> practice"
>>
>> I have supplied this data to the recommender in the past and it has
>> worked successfully. Can you please advise if there is a fault at the
>> moment?
>>
>> Thanks and regards,
>>
>> Phil
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632
>>
>>
>>
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