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

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Sep 10 11:22:14 PDT 2021


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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