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[bioontology-support] Annotator returning a lot of duplicate results

Trish Whetzel whetzel at stanford.edu
Wed Mar 17 01:19:14 PDT 2010


Hi Joey,

A fix has been implemented to resolve this issue.

Trish


On Mar 12, 2010, at 12:17 PM, Joey Geiger wrote:

> The annotator is returning a lot of duplicate results for queries.  
> Some are Automatic and some are Manual but even with that difference  
> they are duplicated.
>
>
> http://rest.bioontology.org/test_oba.html
>
> params (different from default)
> minTermSize: 2
> ontologiesToKeepInResult: 1000
> isVirtualOntologyId: true
> levelMax: 10
> textToAnnotate: Effect of DES-treated Ept congenic rat lung lines on  
> gene expression in the anterior pituitary gland Ept9 DES-treated  
> replicate 1 left lung
> format: text
>
> Example result (snipped):
>
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Manual, termName  
> = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Manual, termName  
> = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Automatic,  
> termName = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Automatic,  
> termName = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Manual, termName  
> = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Automatic,  
> termName = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Manual, termName  
> = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Manual, termName  
> = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Automatic,  
> termName = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Manual, termName  
> = Anterior Pituitary Gland, from = 77, to = 100]
> ], AnnotationBean [
> 		score = 3696
> 		concept = [localConceptId: 42311/MA:0000177, conceptId: 3272822,  
> localOntologyId: 42311, isTopLevel: 1, preferredName:  
> adenohypophysis, synonyms: [], semanticTypes: [[id: 5132234,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/ 
> Anterior_Lobe_of_the_Pituitary_Gland, mappingType = Manual, termName  
> = Anterior Pituitary Gland, from = 77, to = 100]
>
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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