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[bioontology-support] [POSSIBLE VIRUS:###] Re: reg. bioportal webservices

Paul R Alexander palexander at stanford.edu
Wed Apr 21 23:39:31 PDT 2010


Trish and Sridevi,

I'm attaching a modified version of the quick_jump and form_complete 
widgets for use with the staging server. If you need to modify it again, 
look for the following line:

// Set the search server to the UI installation of BioPortal that you 
want to search
var searchServer = "http://stage.bioontology.org";

You can set the server to use here, note that it needs to point to a 
BioPortal UI installation (http://stage.bioontology.org or 
http://bioportal.bioontology.org).

Please let me know if you have any other questions.

Paul

On 4/21/10 9:35 PM, Trish Whetzel wrote:
> 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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> bioontology-support at lists.stanford.edu
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