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[bioontology-support] [BioPortal] Feedback from Karin Colsman

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Aug 25 13:21:44 PDT 2020


Hello Karin,


On Aug 24, 2020, at 2:24 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Dear support team,

we uploaded a TTL file, and some of the properties are missing their labels.

https://bioportal.bioontology.org/ontologies/AFO/?p=properties

I have double-checked the file, and the entities do have a skos:prefLabel defined in our source file.

http://purl.allotrope.org/voc/afo/merged/REC/2020/06/merged-and-inferred.ttl

Is there anything we can do to help fix this bug?



I spent some time yesterday investigating the portion of the source code that sets human readable labels for ontology classes and properties. For classes, the logic is more involved and looks at several locations for label values, including rdfs:label, skos:prefLabel, and http://data.bioontology.org/metadata/def/prefLabel. However, the code for properties is more simplistic and only checks for rdfs:label values.

To see a concrete example, you can look at the property tree for the Biomedical Resource Ontology:

https://bioportal.bioontology.org/ontologies/BRO/?p=properties

BioPortal displays human readable labels for each node in the tree because the source ontology stored those values in an rdfs:label for each property.

It appears that the human readable labels for your properties are stored in skos:prefLabel, which is why they aren’t getting picked up and displayed by BioPortal. I’ve entered an enhancement request in our issue tracker to add skos:prefLabel as one of the locations to check for human readable property labels:

https://github.com/ncbo/ontologies_api/issues/70

I don’t have a definitive answer at the moment for where this issue will end up in the queue. If you have an urgent need for this functionality, a workaround would be to modify your ontology to add your labels in rdfs:label for each property.

Kind regards,
Jennifer

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