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[bioontology-support] need an Ontology..

Trish Whetzel whetzel at stanford.edu
Fri May 21 14:32:16 PDT 2010


Hi Nooshin,

How are things going with the Annotator?

Trish


On May 19, 2010, at 1:06 AM, Clement Marie Jonquet wrote:

> Hi Nooshin,
>
> I think you are doing good. Except the ontologiesToExpand that is  
> useless
> if mappingTypes=null.
> Give me some of the text you want to annotate.
>
> For " rosette carbon night " I get an annotation with 42737/PO: 
> 0008034:
>
> AnnotationBean [
> 		score = 8
> 		concept = [localConceptId: 42737/PO:0008034, conceptId:
> 7520093, localOntologyId: 42737, isTopLevel: 0, fullId:
> http://purl.obolibrary.org/obo/PO_0008034, preferredName: leaf whorl,
> definitions: [], synonyms: [rosette], semanticTypes: [[id: 10199626,
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MGREP(true), from = 1, to = 7, [name: rosette,
> localConceptId: 42737/PO:0008034, isPreferred: false, dictionaryId:  
> 3], ]
> ]
>
> For carbon and night, it appears they are not in the ontology (as
> confirmed by our search service):
> http://rest.bioontology.org/bioportal/search/carbon/?ontologyids=1108,1038
> ,1036&isexactmatch=1
> http://rest.bioontology.org/bioportal/search/night/?ontologyids=1108,1038 
> ,
> 1036&isexactmatch=1
> http://rest.bioontology.org/bioportal/search/rosette/?ontologyids=1108,103
> 8,1036&isexactmatch=1
>
> Clement
>
> -----Original Message-----
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Saturday, May 15, 2010 1:36 AM
> To: omranian at uni-potsdam.de; Clement Jonquet
> Cc: support
> Subject: Re: [bioontology-support] need an Ontology..
>
> 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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