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[bioontology-support] [BioPortal] Feedback from nlorimer
nlorimer at stanford.edu
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 stanford.edu <http://stanford.edu>).
> Also, did you still want to have this ontology in the Biblio slice as
> you mentioned previously below?
> Kind regards,
>> On Aug 28, 2017, at 2:55 PM, Nancy Lorimer <nlorimer at stanford.edu
>> <mailto:nlorimer at stanford.edu>> 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.
>> On 6/16/2017 1:27 PM, Jennifer Leigh Vendetti wrote:
>>> Hi Nancy,
>>>> On Jun 16, 2017, at 1:05 PM, support at bioontology.org
>>>> <mailto:support at bioontology.org> wrote:
>>>> Name: nlorimer
>>>> Email: nlorimer at stanford.edu <mailto:nlorimer at stanford.edu>
>>>> Location: http%3A%2F%2Fbioportal.bioontology.org
>>>> 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
>>> 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 stanford.edu <http://stanford.edu/>). 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,
>> Nancy Lorimer
>> Head, Metadata Dept
>> Stanford University Libraries
>> nlorimer at stanford.edu
Head, Metadata Dept
Stanford University Libraries
nlorimer at stanford.edu
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