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[bioontology-support] [Biomodels-net-support] bioportal/ mapping

N Juty juty at
Mon Oct 28 03:33:08 PDT 2013

Hi Maxwell,

You should also bear in mind that not all of the BioPortal Ontologies 
are in the Registry. If there are any particular ones 
that you would like to see added, please let us know. We do have some 
requirements that should be met when adding new data collections to our 
Registry, such as identifier stability (eg. between releases), and 
suitably maintained data/resources. The FAQ for such requirements, 
though in need of some update, can be found here:



On 28/10/13 09:56, Camille Laibe wrote:
> Dear Maxwell,
> Unfortunately, there is currently no code or web services which would
> directly provide the mapping you are looking for.
> However, this is one of the new features we are working on: provide a
> way to convert between different URI schemes (such as BioPortal and
> URIs). I expect this to be released early next year.
> In the meantime, you can use the XML or RDF export of the Registry [1]
> to extract this mapping.
> Hope this helps.
> [1]
> On 28/10/13 02:27, Maxwell Neal wrote:
>> Hi,
>> I was wondering - is there code or a web service that provides mappings
>> between BioPortal URI's to their equivalent
>> <> URI's?
>> I'm working on a Java program that will need to convert a bunch of
>> BioPortal URI's to <> URI's, and
>> vice versa.
>> Many thanks!
>> M
>> ---------------------------------
>> Maxwell Neal
>> Post-doctoral researcher
>> Department of Bioengineering
>> University of Washington
>> mneal at <mailto:mneal at>
>> ---------------------------------

Nick Juty
BioModels Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
United Kingdom
Cambridge CB10 1SD

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