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[bioontology-support] [BioPortal] Feedback from Clement Jonquet

Paul R Alexander palexander at
Mon Jun 23 11:37:20 PDT 2014

Thanks for reporting this. By default, we only return one class per match per ontology when using longest-only. We haven’t seen much of a use case for doing otherwise because we felt that ontologies typically wouldn’t have overlapping concepts. However, I’ve created an issue for us to investigate doing something better than choosing the first class from the results, which I believe is what we’re doing now.


On Jun 23, 2014, at 4:30 AM, support at wrote:

> Name: Clement Jonquet
> Email: jonquet at
> Location:
> Comment:
> While testing the new longets only parameter of the Annotator we found out something strange:
> Try to annotate the text "cell" with ontology MESH. 
> longestOnly=false returns 2 annotations
> while
> longestOnly=true returns 1 annotation .
> Cell (T025)...
> It seems there is something weird (maybe because the annotation  remove is a semantic type... 
> Can you reproduce and tell us more.
> Clement and Soumia
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

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