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[bioontology-support] [BioPortal] Feedback from nlorimer

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Aug 28 18:35:41 PDT 2017


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,
Jennifer


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.

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 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<http://2fbioportal.bioontology.org/>%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 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,
Jennifer




--
Nancy Lorimer
Head, Metadata Dept
Stanford University Libraries
nlorimer at stanford.edu<mailto:nlorimer at stanford.edu>
650-725-8819

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