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

Mark Williams mwilliam at ebi.ac.uk
Thu Dec 3 01:11:05 PST 2015


Thanks Michael.

On 02/12/2015 19:20, Michael Dorf wrote:
> Hi Mark,
>
> The Mass Spectrometry ontology is fixed as well. I've checked for 
> 'Electron ionization', and it's now found:
>
> http://bioportal.bioontology.org/search?q=Electron%20ionization&ontologies=MS
>
> As always, please notify us of any other issues you encounter with the 
> site or the API.
>
> Thanks!
>
> Michael
>
>
>> On Dec 2, 2015, at 01:56, Mark Williams <mwilliam at ebi.ac.uk 
>> <mailto:mwilliam at ebi.ac.uk>> wrote:
>>
>> 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> 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
>>>>>>
>>>>>>
>>>>>> *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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