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[bioontology-support] [External] Re: [BioPortal] Feedback from fergusonch

Ferguson, Christopher [USA] Ferguson_Christopher at
Mon Apr 29 13:26:00 PDT 2019

Hi Jennifer,

Thank you again. I did try resubmitting an OWL file into another test and had it load fine. I’m not sure what the problem was with my earliest attempted submissions, but I’ll be sure to convert from TTL to OWL prior to submission in the future. One thing I did notice though is that the annotation properties are duplicated (PATEpiTest Ontology), is that because I provided the URIs for the respective properties during the submission process? (i.e. I entered for Preferred Label and now see “Preferred Name” and “Label” in the Class viewer)

Thank you,

From: Jennifer Leigh Vendetti <vendetti at>
Date: Monday, April 29, 2019 at 3:36 PM
To: "Ferguson, Christopher [USA]" <Ferguson_Christopher at>
Cc: "support at" <support at>
Subject: Re: [External] Re: [bioontology-support] [BioPortal] Feedback from fergusonch

Hi Chris,

On Apr 29, 2019, at 7:17 AM, Ferguson, Christopher [USA] <Ferguson_Christopher at<mailto:Ferguson_Christopher at>> wrote:

Thank you for your help! I do see that the last one of the list of submissions parsed, though I seem to recall having a problem with getting the classes for that one to load which is why I started creating the smaller test files that are currently populating the Classes tab.

I uploaded the OWL file you sent and BioPortal processed it without issue. The class tree is fully available in the application. If you upload a new / complete version of your ontology instead of the test file you mention above and have an issue viewing the classes, let us know and we can take a look at it.

I have attached the most recently submitted file (.ttl) and a .owl version of that file. Being able to submit the TTL files would be beneficial, as we maintain our terminologies in that format, but converting to OWL is not a problem.

Our system is currently architected to accept submissions from end users in OWL, OBO, or SKOS. We’ll need you to do the conversion from TTL to OWL in order to submit to BioPortal.

Kind regards,

Thank you,

From: Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>>
Date: Friday, April 26, 2019 at 6:57 PM
To: "support at<mailto:support at>" <support at<mailto:support at>>
Cc: "Ferguson, Christopher [USA]" <Ferguson_Christopher at<mailto:Ferguson_Christopher at>>
Subject: [External] Re: [bioontology-support] [BioPortal] Feedback from fergusonch

Hello Chris,

We accept ontologies in OWL, OBO, or SKOS. Could you send me a copy of the OWL file that you’d like to load in BioPortal? I see you submitted one earlier that parsed, but I assume that’s not your latest version. Doing a conversion to TTL isn’t necessary / desirable.

Kind regards,

On Apr 24, 2019, at 7:04 AM, support at<mailto:support at> wrote:

Name: fergusonch
Email: ferguson_christopher at<mailto:ferguson_christopher at>

I am created a private test ontology (acronym: PTEST/name: PAT Test) in anticipation for a new public submission, but I am running into errors trying to get the classes to display. I had initially tried a terminology I created in Protege, but ran into a problem with retrieving classes after upload (uploaded as a .owl file). I think created a smaller test file in WebProtege, which worked and is currently what occupies the Classes tab. I made some changes to my original ontology in an effort to address the problem, but now that ontology has the status of "Uploaded, Error Rdf". I did try uploading a .ttl file most recently, but it was an output from Protege so I was hoping that wasn't a problem.
Sorry for the long comment, just wanted to give as much detail as possible. I was hoping to get some guidance on what features of my ontology might be causing the problem with prasing, indexing and class retrieval. Any guidance you can provide would be greatly appreciate!
Thank you,
Email: ferguson_christopher at<mailto:ferguson_christopher at>

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