Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] ontology mappings

Clement Jonquet jonquet.lirmm at
Tue Feb 13 11:00:06 PST 2018

Hi Michel, 

NCBO and us do not have a lot of documentation about mappings. A small technical explanation is here: <>

On the "recognized’’ point: 
BioPortal does not automatically extract/recognize mappings that would be in described inside the ontologies. Except if the class explicitly uses the same URI or has a CUI property described properly (as documented in the link). 

If an ontology file contains "mappings" represented with SKOS matching properties or owl:sameAs or any other specific property (e.g., OBO-XREF), those mappings will not be extracted by AgroPortal. 

It sounds weird, but there are multiple historical reasons for this including the fact that at the beginning of the NCBO project, one would not always expect the mapped ontologies to be « already » in BioPortal. This situation is not always true, but now there is a strong chance  the mapped ontologies are already on BioPortal. 
Within AgroPortal we removed that constraint a couple of years ago (external mappings) and will start soon working (again) on mappings with Elcio (CC) who just join us at LIRMM.

As of now, I would recommend to use SKOS properties inside you SIO file to represent mappings. Those would be considered by the new parser for sure.


> Le 13 févr. 2018 à 00:59, Michel Dumontier <michel.dumontier at> a écrit :
> Hi!
>   Can you point me to public documentation that describes how my ontology (SIO) can be annotated with mappings that can be recognized by the BioPortal system?
>   thanks!
> m.
> -- 
> Michel Dumontier
> Distinguished Professor of Data Science
> Maastricht University
> <>_______________________________________________
> bioontology-support mailing list
> bioontology-support at

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list