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[bioontology-support] Tools and scripts to generate mappings in a VA

Paul R Alexander palexander at
Fri Jul 11 15:11:57 PDT 2014

We don’t have any existing scripts that can handle mapping generation. We are working on re-engineering the way we handle mappings within the BioPortal infrastructure so that things like OBO xref and LOOM won’t be materialized, just provided as a part of a query response on the fly. Both of the cases you describe will be handled with this new process and you won’t have to run anything to get the mappings, just make the appropriate REST calls to pull them out.

This should be ready for our production system sometime in the next 2-3 months with a release to the Virtual Appliance after that.


On Jul 11, 2014, at 9:47 AM, Clement Jonquet <jonquet at> wrote:

> Hi all,
> I am wondering where are the scripts/tools you guys used to generate mappings btw ontologies.
> Are they somewhere on GitHub or in the VA ?
> For instances:
> - I am hosting several OBO ontologies in my local appliance and they contains “xref:” properties that represent mappings to other ontologies.
> - I am hosting several UMLS ontologies that offer cui property that that represent mappings to other ontologies.
> Are those scripts available ?
> Can some of them be automated when an ontology is parsed to be included in BioPortal ?
> Thank you
> Clement
> ---------------------------------------------------------------------------------------------------------------------------
> Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
> PI of the SIFR project: Semantic Indexing of French Biomedical Data Resources (ANR, UM2, CNRS, IBC)
> Organizer of Web Science Montpellier Meetup
> jonquet at
>                 University of Montpellier                          Tel:                      +33/4 67 14 97 43
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