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

Sridevi Polavaram spolavar at gmu.edu
Thu Apr 22 06:20:08 PDT 2010


Thanks Alexander. The fill in the field widget seems to be working fine 
now.
Trish, I will let you know when I am ready to use the main server.
Thanks
Sridevi


Paul R Alexander wrote:
> 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
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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