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

Joey Geiger jfgeiger at mcw.edu
Fri Mar 12 12:17:53 PST 2010


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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