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[bioontology-support] programmatic class mappings

John Graybeal jgraybeal at
Thu Aug 30 16:14:16 PDT 2018

Hi Ross,

BIoPortal's treatment of mappings is described in 

Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept.  At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.)

But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example

>  You can also manually create mappings using our REST API:
> We have example code for programmatically creating mappings in our GitHub sample code repository:

I hope all this helps.


> On Aug 28, 2018, at 12:02 PM, Filice, Ross W <Ross.W.Filice at> wrote:
> Hi – in an OWL submission what is the appropriate property to map classes across ontologies? I’ve tried owl sameAs but I don’t know that it’s working. Should we be using skos:exactMatch instead? Or other?
> And similarly is there a way to map subclasses across ontologies?
> Thanks much,
> Ross
>   Ross W. Filice, M.D.
>   Associate Professor and Chief, Imaging Informatics
>   Department of Radiology, MedStar Georgetown University Hospital
>   Chief, Imaging Informatics
>   MedStar Medical Group Radiology
>   Clinical Informatics Scientist
>   National Center for Human Factors in Healthcare, MedStar Institute for Innovation
>   3800 Reservoir Road NW, CG 201
>   Washington DC, 20007
>   202-444-3450 PHONE
>   202-444-4899 FAX
>   ross.w.filice at
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> bioontology-support mailing list
> bioontology-support at

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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