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[bioontology-support] [BioPortal] Feedback from Vertebrate Trait

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Sep 10 14:49:25 PDT 2021


Hi Cari,

It looks like correcting the header tag and re-uploading has allowed the ontology to fully process in our system. I’m able to see / navigate the classes now. You may have to refresh your browser to see the same.

Kind regards,
Jennifer


On Sep 10, 2021, at 12:36 PM, Park, Cari [AN S] <caripark at iastate.edu<mailto:caripark at iastate.edu>> wrote:

Hi Jennifer,

Thank you for getting back to me. I would prefer to use the OBO file, but tried to upload the OWL version to see if it would work (clearly, I should have checked it first). Yes, I would appreciate it if you would delete the failed submission attempts. I have corrected the header tag issue and attempted to re-load the OBO file, so hopefully that works.

Thanks again,
Cari

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Friday, September 10, 2021 at 1:22 PM
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: "Park, Cari [AN S]" <caripark at iastate.edu<mailto:caripark at iastate.edu>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Vertebrate Trait

Hello Cari,



On Sep 10, 2021, at 7:36 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:
Hello,
I have uploaded several versions of the Livestock Product Trait Ontology (LPT; https://bioportal.bioontology.org/ontologies/LPT) and continue to get an error on the version submission line ("Uploaded, Error RDF"). How can I go about getting this fixed so the ontology can be browsed?



I spent some time looking at your ontology submissions this morning. I noticed in your GitHub repository you have both OWL and OBO formats of your ontology:

https://github.com/AnimalGenome/livestock-product-trait-ontology/tree/master/current_release

It’s not clear to me which you prefer to have in BioPortal. The OBO version of your ontology isn’t parsing because you have an error in your header tags. On line 11, the "data-version" header tag has a space character in it instead of a dash:

https://github.com/AnimalGenome/livestock-product-trait-ontology/blob/30f8264911026f1f2c0b4aae27f7feea1ff365f9/current_release/lpt.obo#L11

Here’s a link to the section in the OBO file format specification on document header tags:

https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1

This applies to the submissions you created marked as versions 2.2 (uploaded January 11th) and 3.1 (uploaded September 8th).

Your latest upload attempt from September 9th didn’t parse because it’s an HTML file, not an ontology file. If you download the file you can see what I mean.

If you’d like, I could delete these last 3 submission attempts that failed to parse. Also, if you let me know which format you want in BioPortal (OWL or OBO), I could try doing the upload on your behalf to make sure it goes smoothly this time.

Kind regards,
Jennifer

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