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[bioontology-support] Help with expression (cutoff)

Paul R Alexander palexander at stanford.edu
Wed May 9 15:41:27 PDT 2012


This is fixed for all future uploads and no action is needed on your 
part. It was an issue with encoding our output that was causing the problem.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 5/9/12 1:06 PM, Rob Wynden wrote:
> Is this fixed for all future uploads also?
> Thanks!
> Rob
>
>
> On 5/9/12 1:04 PM, Mobed, Ketty wrote:
>> Thanks Trish. Yes, I saw. This was fast!
>>
>> There are several other expression like this, have they all now been 
>> fixed or should I send you the specific instances to be fixed internally?
>>
>> Thanks again,
>> Ketty
>>
>> ------------------------------------------------------------------------
>> *From:* Trish Whetzel [whetzel at stanford.edu]
>> *Sent:* Wednesday, May 09, 2012 1:01 PM
>> *To:* Wynden, Rob; Mobed, Ketty
>> *Cc:* support at bioontology.org Support
>> *Subject:* Re: Help with expression (cutoff)
>>
>> The expression is now correctly displayed in the UI:
>> http://bioportal.bioontology.org/ontologies/47403/?p=terms&conceptid=MM_CLASS_101
>>
>> Trish
>>
>>
>> On May 9, 2012, at 10:06 AM, Rob Wynden wrote:
>>
>>> We are supposed to engage Allen by Friday of this week.
>>>
>>> Rob
>>>
>>>
>>>
>>> On 5/9/12 10:02 AM, Trish Whetzel wrote:
>>>> Thanks for the additional information. I didn't realize these 
>>>> values need to be curated. To help prioritize the issue, is this a 
>>>> blocker for your work and when will you be working with Barry to 
>>>> review this values?
>>>>
>>>> Trish
>>>>
>>>>
>>>> On May 9, 2012, at 9:53 AM, Rob Wynden wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Well we can't curate HOM Bool expressions on BioPortal if folks 
>>>>> can't read them.  We are about to start working in with Barry 
>>>>> Smith's team.  This could hold up the train.
>>>>>
>>>>> Rob
>>>>>
>>>>>
>>>>>
>>>>> On 5/9/12 9:50 AM, Trish Whetzel wrote:
>>>>>> Hi Rob and Ketty,
>>>>>>
>>>>>> It looks like there is an issue rendering the expression in the 
>>>>>> Web interface since the "Get Term" web service call returns the 
>>>>>> expression [1] and also calling the "Get Term" web service from 
>>>>>> Excel GoogleDocs also returns the expression. I'll submit a bug 
>>>>>> report related to the rendering issue. Can you confirm this using 
>>>>>> this ontology is working properly in your application?
>>>>>>
>>>>>> Trish
>>>>>>
>>>>>> [1] 
>>>>>> http://rest.bioontology.org/bioportal/concepts/47403?conceptid=MM_CLASS_101&apikey=YourAPIKey
>>>>>>
>>>>>>
>>>>>> On May 9, 2012, at 9:22 AM, Rob Wynden wrote:
>>>>>>
>>>>>>> I think that we may be triggering an escape character on the 
>>>>>>> page.  Is that correct?
>>>>>>> Rob
>>>>>>>
>>>>>>>
>>>>>>> On 5/9/12 8:57 AM, Mobed, Ketty wrote:
>>>>>>>> Hi Trish,
>>>>>>>>
>>>>>>>> here is a problem that I have run into. I have attached the 
>>>>>>>> Protege generated .owl file for HOM-ORTHO (BP ID# 1697). When 
>>>>>>>> you open up the Protege owl file and click on the left to open 
>>>>>>>> OrthoSurgery -> Diagnoses -> Comorbidities -> Anemia, then on 
>>>>>>>> the right hand side the expression for HOM-BOOL1 reads 
>>>>>>>> (I9CM>I9CM.2799 AND I9CM<I9CM.2860), and this is correct. Now 
>>>>>>>> when I upload the HOM-ORTHO.owl file to BP, then when you 
>>>>>>>> expand the ontology to Anemia you see that Hom Bool1 was 
>>>>>>>> cut-off and only reads (I9CM>I9CM.2799 AND I9CM  .
>>>>>>>>
>>>>>>>> Why is this? This is the SQLite syntax that we need to process 
>>>>>>>> our HOM translator. Any help will be appreciated.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Ketty
>>>>>>>>
>>>>>>>> 'It's the little things that matter'
>>>>>>>>
>>>>>>>> Ketty Mobed, PhD
>>>>>>>> UCSF-IHPS-Informatics Lab
>>>>>>>> ketty.mobed at ucsf.edu
>>>>>>>> 415-352-8815
>>>>>>
>>>>>>
>>>>
>>>>
>>
>>
>
>
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