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[bioontology-support] [BioPortal] Feedback from Benjamin Leinfelder

Ray Fergerson ray.fergerson at
Tue Dec 16 15:52:06 PST 2014

Handling directly with XiXi.


-----Original Message-----
From: Ben Leinfelder [mailto:leinfelder at] 
Sent: Monday, December 15, 2014 11:50 AM
To: Ray Fergerson
Cc: support at
Subject: Re: [bioontology-support] [BioPortal] Feedback from Benjamin

Hi Ray,
A colleague of mine, Xixi Luo, wants to explore deploying an instance of
BioPortal locally but can't seem to locate the virtual appliance download.
Can you assist us with finding that?

On Dec 10, 2014, at 3:10 PM, Ray Fergerson <ray.fergerson at>

> Looks like the private option will be fine. Yes your api key provides 
> access to your private ontologies, search, etc. If you want more than 
> one person/application to access the private information, just put 
> their user name in the access control list for the private ontology.
> Ray
> -----Original Message-----
> From: Ben Leinfelder [mailto:leinfelder at]
> Sent: Wednesday, December 10, 2014 11:00 AM
> To: Ray Fergerson
> Cc: support at
> Subject: Re: [bioontology-support] [BioPortal] Feedback from Benjamin 
> Leinfelder
> Hi Ray,
> I'm inclined to start with the first option and just keep our ontology 
> private.
> I don't expect our UI development work to overload the services, but 
> we are also looking at using the recommender service for automated 
> classification If we end up doing too many queries, please let us know.
> I assume my API key will still allow me to interact with private 
> ontologies (find concept matches, navigate classes, etc)?
> Thanks!
> -ben
> On Dec 9, 2014, at 5:46 PM, Ray Fergerson <ray.fergerson at>
> wrote:
>> There are two ways forward here. First you can load your ontology as 
>> "private". Then only you and those you specify will be able to see it.
>> The second way is to set you your own virtual machine instance of
> BioPortal.
>> If you are going to be (1) doing lots of queries or (2) making lots 
>> of modification (notes & mappings) then the second method is
>> If not then you can use the first.
>> When the ontology is complete you can change it over to public if you 
>> choose.
>> Ray
>> -----Original Message-----
>> From: bioontology-support
>> [mailto:bioontology-support-bounces at] On Behalf Of 
>> support at
>> Sent: Monday, December 8, 2014 2:32 PM
>> To: support at; leinfelder at
>> Subject: [bioontology-support] [BioPortal] Feedback from Benjamin 
>> Leinfelder
>> Name: Benjamin Leinfelder
>> Email: leinfelder at
>> Location:
>> Comment:
>> I'm wondering if there's a development instance of BioPortal that 
>> could be used for testing the API with some not-yet-finished 
>> ontologies. We really like BioPortal and don't want to pollute the 
>> holdings with works-in-progress.
>> Thanks,
>> -ben
>> NCEAS software development
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at

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