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[bioontology-support] [BioPortal] Feedback from Paola Roncaglia

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Jun 9 10:22:52 PDT 2020


Hello Paola,



On Jun 9, 2020, at 2:59 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


I'd need to download the CSV file of the latest release of UBERON please.

I looked at the Submissions panel in https://bioportal.bioontology.org/ontologies/UBERON/?p=summary, but I suspect there are some issues with version numbers and release dates (compare with https://uberon.github.io/). I contacted UBERON in case anything needs to be fixed at the source (https://github.com/obophenotype/uberon/issues/1617). In the meantime, would you please be able to confirm if the CSV file in the top line in the BioPortal page is indeed the version that was released on 2019-11-22?



I downloaded the latest submission of UBERON and looked at the ontology source file. I can confirm that it’s the version you requested, i.e.:

…
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/ext.owl">
  <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/releases/2019-11-21/ext.owl”/>
...

The contents of the Version column is misleading, and a product of the fact that BioPortal checks for version numbers in OWL ontologies by examining the owl:versioninfo property. UBERON uses the owl:versionIRI property, which is why you don’t see the value of this property reflected in the Version column. There are a couple of issues in our GitHub repositories that provide more detail:

https://github.com/ncbo/bioportal-project/issues/168
https://github.com/ncbo/owlapi_wrapper/issues/11

Hope that information helps.

Kind regards,
Jennifer

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