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[bioontology-support] [BioPortal] Feedback from nlorimer

Nancy Lorimer nlorimer at
Mon Aug 28 21:40:14 PDT 2017

Huh, it just took a really long time, and I seem to have pulled in the 
BF base as well, which I didn't quite want. Comes from using the Protege 
file, I guess. I do manage to find something wrong to do!

On Github, it is at 
Would I use that URL?

thanks and sorry for being so dumb about this


On 8/28/2017 6:35 PM, Jennifer Leigh Vendetti wrote:
> Hi Nancy,
> The latest version of the PMO ontology shows as successfully parsed in 
> BioPortal. I looked at the submission information though, and the last 
> submission appears to have been a file upload. If you want to have it 
> pulled from GitHub, could you send the URL of the ontology in GitHub? 
> You can send it to me privately if that’s sensitive information 
> (vendetti at <>).
> Also, did you still want to have this ontology in the Biblio slice as 
> you mentioned previously below?
> Kind regards,
> Jennifer
>> On Aug 28, 2017, at 2:55 PM, Nancy Lorimer <nlorimer at 
>> <mailto:nlorimer at>> wrote:
>> Hi Jennifer,
>> I went on hiatus with this again, and tried once more to load and got 
>> nowhere. Obviously, I'm doing something wrong. My ontology is in 
>> Protege and it is in GitHub. Perhaps if you could direct me to what 
>> URL I am supposed to use? I feel like I've tried them all, but 
>> clearly haven't hit the right one or am trying to load it the wrong way.
>> thanks
>> Nancy
>> On 6/16/2017 1:27 PM, Jennifer Leigh Vendetti wrote:
>>> Hi Nancy,
>>>> On Jun 16, 2017, at 1:05 PM, support at 
>>>> <mailto:support at> wrote:
>>>> Name: nlorimer
>>>> Email: nlorimer at <mailto:nlorimer at>
>>>> Location: 
>>>> <>%2Fontologies%2FPMO
>>>> *Feedback:*
>>>> Hi, I tried way to early on to load the Performed Music Ontology 
>>>> (part of the LD4P project in the libraries). It never did load 
>>>> properly.
>>> I looked at the PMO ontology in BioPortal. The ontology never loaded 
>>> because the URL specified in the “Load from URL” section resolves to 
>>> a 404 error. If you’d like BioPortal to load your ontology from a 
>>> URL, the URL must point to the exact location of the file (with the 
>>> file name included). I noticed that PMO has a viewing restriction of 
>>> private. You’re welcome to send us the correct URL via private email 
>>> (vendetti at <>). We could enter it 
>>> on your behalf and reprocess the ontology. Alternatively, you could 
>>> navigate to your ontology summary page and click the “Edit 
>>> submission information” link to show the form that would allow you 
>>> to enter a valid file location.
>>>> I'd like to get rid of it and start again in the Biblio slice. 
>>>> Could you just delte this for me?
>>> We can add ontologies to a slice retroactively after they’ve been 
>>> created in BioPortal. Would you like us to assist you in resolving 
>>> the loading issue and add PMO to the Biblio slice? I think we can 
>>> repair the current entry without needing to do a deletion.
>>> Kind regards,
>>> Jennifer
>> -- 
>> Nancy Lorimer
>> Head, Metadata Dept
>> Stanford University Libraries
>> nlorimer at
>> 650-725-8819

Nancy Lorimer
Head, Metadata Dept
Stanford University Libraries
nlorimer at

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