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[bioontology-support] config for my own PURL server

Paul R Alexander palexander at
Tue Oct 15 12:05:23 PDT 2013

Yes, handing for URIs in OWL files hasn't changed.

On October 13, 2013 at 9:19:24 AM, Trish Whetzel (plwhetzel at wrote:

Is it still the case that URIs for ontologies in the OWL format are displayed as provided in the OWL file?


On Fri, Oct 11, 2013 at 10:15 AM, Paul R Alexander <palexander at> wrote:

We use the OBO Foundry id policy to generate URIs for the full id. This is handled in code so there is no configuration option that would allow you to override the method used to generate the id, it would require changing the code itself by hardcoding your ontology id (or change the method used for all ontologies).

Future versions of the appliance may work better with OBO ontologies where proper idspace mappings exist, though I don't think we've done any extensive testing in this area.


On Oct 11, 2013, at 7:44 AM, "Holt, Jonathan" <jonathan.holt at Vanderbilt.Edu> wrote:

I need help configuring my VM appliance to use my own PURL server. 

I am editing in OBO-edit,  after I upload my ontology to my VM appliance, it create a new Full ID that points to the OBOfoundry site.  Since I haven't yet created a namespace with OBOfoundry, this is causing problems. 

How do I configure the NCBO application to use my own PURL server and not the OBOfoundry site or the bioportal site? 



Jonathan Holt, DO, MS

Assistant Professor of Biomedical Informatics and Medicine
Departments of Biomedical Informatics & Medicine, Division of Genetic Medicine
Vanderbilt University Medical Center
2209 Garland Ave
412 Eskind Biomedical Library
Nashville, TN  37232-8340
Phone:  615-322-8683
Fax: 615-875-1424

jonathan.holt at

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