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

Michael Dorf mdorf at
Wed Dec 2 11:20:34 PST 2015

Hi Mark,

The Mass Spectrometry ontology is fixed as well. I've checked for 'Electron ionization', and it's now found:

As always, please notify us of any other issues you encounter with the site or the API.



On Dec 2, 2015, at 01:56, Mark Williams <mwilliam at<mailto:mwilliam at>> wrote:

Thank you.



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.



On Nov 25, 2015, at 01:09, Mark Williams <<mailto:mwilliam at>mwilliam at<mailto:mwilliam at>> wrote:

Thanks Michael.

Much appreciated.



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.


Michael Dorf

On Nov 24, 2015, at 07:26, <mailto:support at> support at<mailto:support at> wrote:

Name: Mark Williams

Email: mwilliam at<mailto:mwilliam at>



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.

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