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[bioontology-support] reg. bioportal webservices

Trish Whetzel whetzel at
Wed Apr 21 18:06:13 PDT 2010

Hi Sridevi,

The file can be viewed at: 
42702. If you register for an account using the Stage server, we can  
transfer 'ownership' of the ontology to your account and that will  
allow you to upload subsequent versions to the Stage server for review  
as you develop the final version of your NCBI taxonomy subset.   
However, please do keep in mind that the Stage server may not always  
be accessible.


On Apr 21, 2010, at 1:27 PM, Sridevi Polavaram wrote:

> Hi Trish,
> Sure. Here is the attachment. Please let me know when it is ready.  
> However, it would be helpful if you can also let me know how I  
> should upload later versions subsequently. As I said, this is only  
> the first version and I will be adding more terms to it in the next  
> versions while testing. I really appreciate for your help and prompt  
> response to this.
> Best regards,
> Sridevi
> Trish Whetzel wrote:
>> Hi Sridevi,
>> We do have a Staging environment that we can test upload the file,  
>> however at the moment we are also in the process of pushing new  
>> code to this server so it may not be as accessible as usual. Would  
>> you mind sending me the file and I will coordinate with folks here  
>> to upload this to the Stage server?
>> Once the final file is generated, it can be uploaded to BioPortal  
>> as a "view" [1] or subset of the NCBI taxonomy and after processing  
>> the ontology file, within a few hours, it will be accessible for  
>> use via the widgets and Web services.
>> Cheers,
>> Trish
>> [1]
>> On Apr 21, 2010, at 11:23 AM, Sridevi Polavaram wrote:
>>> Hi Trish,
>>> I have made a lighter version of NCBI taxonomy ontology based on  
>>> the species we have in NeuroMorpho.Org and I am doing some quality  
>>> control testing on this. My question is, can I upload this new  
>>> ontology on to bioportal? but I prefer that it is not accessible  
>>> to the public, as it is not yet ready.
>>> My second question is, irrespective of whether I can or cannot  
>>> upload my new obo ontology into a private space, how soon can I  
>>> expect to use the bioportal web services especially fill in a  
>>> field in your form aka auto completion feature and the  
>>> viusalization feature options that you have for the ontology  
>>> widgets. I want to use my own version of ontology for these two  
>>> services. Please let me know how much time should it take to do  
>>> this, if at all possible.
>>> Thanks
>>> Sridevi
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> whetzel at <mailto:whetzel at>
> <NCBI_NMO_taxonomyv1.0.obo>

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