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[bioontology-support] [BioPortal] Feedback from Mark Williams

Mark Williams mwilliam at ebi.ac.uk
Wed Dec 2 01:56:45 PST 2015


Thank you.

Cheers,

Mark

On 01/12/2015 19:33, Michael Dorf wrote:
> Hi Mark,
>
> The term "Homo sapiens" is now found in NCBI Taxonomy after reindexing 
> has been completed. I am still looking into the Mass Spectrometry 
> ontology issue.
>
> Thanks,
>
> Michael
>
>
>> On Nov 25, 2015, at 01:09, Mark Williams <mwilliam at ebi.ac.uk 
>> <mailto:mwilliam at ebi.ac.uk>> wrote:
>>
>> Thanks Michael.
>>
>> Much appreciated.
>>
>> Cheers,
>>
>> Mark
>>
>>
>> On 24/11/2015 19:03, Michael Dorf wrote:
>>> Hi Mark,
>>>
>>> Thank you for reporting this issue. I've taken a look, there appear 
>>> to be two separate problems:
>>>
>>> 1. NCBI - the ontology is working properly, but the term Homo 
>>> sapiens does appear to be missing from our search index. I've kicked 
>>> off a reindexing process, but it does take some time for this 
>>> process to complete. If this doesn't solve the problem, there may be 
>>> a deeper issue to look into on our end. I've created a ticket in our 
>>> bug tracking system (NCBO-1578) that will track this issue. We'll 
>>> try to address it as soon as we can.
>>>
>>> 2. Mass Spectrometry ontology has a wrong pull location set to it, 
>>> pointing to a Github repo instead of the raw ontology file. We'll 
>>> need to either re-point it to a proper location or remove the 
>>> auto-download. A ticket has been created for this as well (NCBO-1579).
>>>
>>> We'll keep you posted once there are resolved.
>>>
>>> Thanks,
>>>
>>> Michael Dorf
>>>
>>>
>>>> On Nov 24, 2015, at 07:26, 
>>>> <mailto:support at bioontology.org>support at bioontology.org wrote:
>>>>
>>>> Name: Mark Williams
>>>>
>>>> Email: mwilliam at ebi.ac.uk <mailto:mwilliam at ebi.ac.uk>
>>>>
>>>> Location: http://bioportal.bioontology.org/search 
>>>> <http://bioportal.bioontology.org/search>
>>>>
>>>>
>>>> *Feedback:*
>>>>
>>>> Searching 'Homo sapiens' does not produce the NCBITAXON term 
>>>> anywhere in the results list.
>>>>
>>>> Also, searching for the term 'Electron ionization' does not show 
>>>> the term from the Mass spectrometry ontology.
>>>>
>>>>
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu 
>>>> <mailto:bioontology-support at lists.stanford.edu>
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>
>

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