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[bioontology-support] reg. bioportal webservices

Trish Whetzel whetzel at stanford.edu
Wed Apr 21 21:35:02 PDT 2010


Sorry about that, I didn't realize that you also want to test this  
version of the ontology with the widgets. The code example points to  
the production server.  I don't know this code well enough to suggest  
changes to have it work with the ontology on the Stage server, but  
Chris (included in this email) will be able to help.

Trish



On Apr 21, 2010, at 9:19 PM, Sridevi Polavaram wrote:

> Hi Trish,
> I tried the auto-completion widget from the http://stage.bioontology.org/ontologies/42702#widgets
> and was testing Example3 in the Fill in a field feature.
> As per the instructions I have downloaded the form_complete.js,  
> which looks very different from the one I got for the NCBI taxonomy  
> widget.
> Next, I have added the following line to my text box in the jsp page.
> <input type="text" name="str" class="bp_form_complete-1453-name"  
> size="50" onfocus="">
>
> But when I execute my application, I don't get the names in the drop- 
> down list anymore. Please, let me know how to fix this.
> Thanks
> Sridevi.
>
> ----- Original Message -----
> From: Trish Whetzel <whetzel at stanford.edu>
> Date: Wednesday, April 21, 2010 9:06 pm
> Subject: Re: reg.  bioportal webservices
>
>> Hi Sridevi,
>>
>> The file can be viewed at: http://stage.bioontology.org/visualize/
>> 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.
>>
>> Trish
>>
>>
>> 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] http://bioportal.bioontology.org/ontologies/38802#views
>>>>
>>>>
>>>> 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 stanford.edu <mailto:whetzel at stanford.edu>
>>>> http://www.bioontology.org
>>>>
>>>>
>>>
>>> <NCBI_NMO_taxonomyv1.0.obo>
>>
>>




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