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[bioontology-support] need an Ontology..

Trish Whetzel whetzel at stanford.edu
Fri May 14 16:36:23 PDT 2010


Hi Nooshin,

Clement and I will take a look into this.

Trish


On May 14, 2010, at 1:41 AM, omranian at uni-potsdam.de wrote:

>
> Dear Trish,
>
> Many thanks for appending these ontologies into the web service.
> I have still problem that I can not get any result when I insert  
> bellow text for annotation with selecting -->
>                  content("longestOnly=false&"
> 			 ."wholeWordOnly=true&"
> 			 ."filterNumber=true&"
> 			 ."scored=true&"
> 			 ."ontologiesToExpand=39183,42736,42737&"
> 			 ."ontologiesToKeepInResult=39183,42736,42737&"
> 	 		 ."textToAnnotate=$text&"
> 			 ."withDefaultStopWords=false&"
>                         ."isStopWordsCaseSenstive=false&"
> 			 ."minTermSize=3&"
> 			 ."withSynonyms=true&"
> 			 ."format=xml&"
> 			 ."levelMax=3&"
> 			 ."mappingTypes=null&");
>
> It should return at least "rosette", "carbon" "night"....but It  
> returns nothing.
> Also for the other text I tried I get nothing or just 1 annotation.
>
> Would you mind please help me in this regard? Maybe I select a wrong  
> ontology or wrong features for annotating.
>
> Thanks a lot for your attention.
>
> Best Regards,
> Nooshin
>
> here is the text I've given for annotating:
>
> "
> Arabidopsis thaliana rosettes were harvested in successive timpoints  
> in an extended night situation.
>
> Usually starch is nearly depleted at the end of the night. To induce  
> a gradual depletion of carbon, we have analysed the global response  
> of transcripts during an extension of the night, where carbon  
> becomes severely limiting from about four hours onwards.
> Keywords: time course
>
> Expression data of Arabidopsis thaliana rosettes in an extended night
>
> 2h before the end of the night
>
> Gene expression data from Arabidopsis rosettes 2h before the end of  
> the night
>
> end of the night A
>
> Gene expression data from Arabidopsis rosettes at the end of the night
>
> end of the night B
>
> Gene expression data from Arabidopsis rosettes at the end of the night
>
> end of the night C
>
> Gene expression data from Arabidopsis rosettes at the end of the night
>
> 2h into an extended night
>
> Gene expression data from Arabidopsis rosettes 2h into an extended  
> night
>
> 4h into an extended nightA
>
> Gene expression data from Arabidopsis rosettes 4h into an extended  
> night
>
> 4h into an extended nightB
>
> Gene expression data from Arabidopsis rosettes 4h into an extended  
> night
>
> 6h into an extended night
>
> Gene expression data from Arabidopsis rosettes 6h into an extended  
> night
>
> 8h into an extended nightA
>
> Gene expression data from Arabidopsis rosettes 8h into an extended  
> night
>
> 8h into an extended nightB
>
> Gene expression data from Arabidopsis rosettes 8h into an extended  
> night
>
> 24h into an extended nightB
>
> Gene expression data from Arabidopsis rosettes 24h into an extended  
> night
>
> 24h into an extended nightC
>
> Gene expression data from Arabidopsis rosettes 24h into an extended  
> night
>
> 48h into an extended nightB
>
> Gene expression data from Arabidopsis rosettes 48h into an extended  
> night
>
> 48h into an extended nightC
>
> Gene expression data from Arabidopsis rosettes 48h into an extended  
> night
> "
>
> Quoting Trish Whetzel <whetzel at stanford.edu>:
>
>> Hi Nooshin,
>>
>> The ontology Plant growth and developmental stage is now accessible  
>> for
>> use via the Annotator. Please refer to the documentation at:
>> http://www.bioontology.org/wiki/index.php/Annotator_Web_service for
>> details on the Web service and drop us a note if you have any  
>> questions.
>>
>> Cheers,
>> Trish
>
>
>




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