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[bioontology-support] Annotator returning different results for the same parameters

Trish Whetzel whetzel at stanford.edu
Tue Apr 27 11:19:25 PDT 2010


Hi Joey,

Thanks for sending this. I talked to the developers and they will take  
a deeper look into this.

Trish


On Apr 27, 2010, at 11:04 AM, Joey Geiger wrote:

> http://rest.bioontology.org/test_oba.html
>
> longestOnly: true
> stopwords:  
> I 
> ,a 
> ,about 
> ,an 
> ,and 
> ,are 
> ,as 
> ,at 
> ,be 
> ,by 
> ,com 
> ,de 
> ,en 
> ,each 
> ,for 
> ,from 
> ,how 
> ,in 
> ,is 
> ,it 
> ,la 
> ,of 
> ,on 
> ,or 
> ,that,the,this,to,was,what,when,where,who,will,with,und,the,www,et,al.
> minTermSize: 2
> withSynonyms: false
> ontologiesToKeepInResult: 1000
> isVirtualOntologyID: true
> textToAnnotate: Heart left ventricle and diaphragm comparison
> format: text
>
> When I use those parameters and I submit the request I get one of  
> the two result sets below. If I hit the back button, change nothing  
> and hit submit again, I might get the other result set or the same  
> one.  Please notice that the first result set includes "heart left  
> ventricle" annotation but the second set does not.
>
>
> Thanks.
>
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_84a4
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(MAPPING, 6) , (ISA_CLOSURE, 0) , (MGREP, 2) ]
> 	parameters = [longestOnly = true, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = false, scored = true,  
> ontologiesToExpand = [], ontologiesToKeepInResult = [1000],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [I, a, about, an, and, are, as, at,  
> be, by, com, de, en, each, for, from, how, in, is, it, la, of, on,  
> or, that, the, this, to, was, what, when, where, who, will, with,  
> und, the, www, et, al.], withDefaultStopWords = false,  
> isStopWordsCaseSenstive = false, text to annotate = Heart left  
> ventricle and diaphragm comparison]
> ]
> 	ontologies = [[Mouse adult gross anatomy, nbAnnotation: 8, score:  
> 444, (42475, 1.203, 1000)]]
> 	annotations = [AnnotationBean [
> 		score = 62
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42470/UBERON:0001103,  
> mappingType = Manual, termName = diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 62
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/Diaphragm,  
> mappingType = Automatic, termName = Diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 62
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 39966/Diaphragm,  
> mappingType = Automatic, termName = Diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 62
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/Diaphragm,  
> mappingType = Manual, termName = Diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 62
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42267/RID1524,  
> mappingType = Automatic, termName = diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 62
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 4525/Diaphragm,  
> mappingType = Automatic, termName = Diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 62
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MGREP(true), [name: diaphragm, localConceptId: 42475/MA: 
> 0001904, isPreferred: true, dictionaryId: 3], from = 26, to = 34]
> ], AnnotationBean [
> 		score = 10
> 		concept = [localConceptId: 42475/MA:0000092, conceptId: 6458474,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0000092,  
> preferredName: heart left ventricle, definitions: [], synonyms:  
> [left ventricle], semanticTypes: [[id: 9119651, semanticType: T999,  
> description: NCBO BioPortal concept]]]
> 		context = [MGREP(true), [name: heart left ventricle,  
> localConceptId: 42475/MA:0000092, isPreferred: true, dictionaryId:  
> 3], from = 1, to = 20]
> ]]
> ]
>
>
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_90e8
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(ISA_CLOSURE, 0) , (MGREP, 0) , (MAPPING, 5) ]
> 	parameters = [longestOnly = true, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = false, scored = true,  
> ontologiesToExpand = [], ontologiesToKeepInResult = [1000],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [I, a, about, an, and, are, as, at,  
> be, by, com, de, en, each, for, from, how, in, is, it, la, of, on,  
> or, that, the, this, to, was, what, when, where, who, will, with,  
> und, the, www, et, al.], withDefaultStopWords = false,  
> isStopWordsCaseSenstive = false, text to annotate = Heart left  
> ventricle and diaphragm comparison]
> ]
> 	ontologies = [[Mouse adult gross anatomy, nbAnnotation: 5, score:  
> 210, (42475, 1.203, 1000)]]
> 	annotations = [AnnotationBean [
> 		score = 42
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42470/UBERON:0001103,  
> mappingType = Manual, termName = diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 42
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/Diaphragm,  
> mappingType = Automatic, termName = Diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 42
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 39966/Diaphragm,  
> mappingType = Automatic, termName = Diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 42
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 42331/Diaphragm,  
> mappingType = Manual, termName = Diaphragm, from = 26, to = 34]
> ], AnnotationBean [
> 		score = 42
> 		concept = [localConceptId: 42475/MA:0001904, conceptId: 6460275,  
> localOntologyId: 42475, isTopLevel: 0, fullId: MA:0001904,  
> preferredName: diaphragm, definitions: [], synonyms: [],  
> semanticTypes: [[id: 9121452, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), mappedConceptID = 4525/Diaphragm,  
> mappingType = Automatic, termName = Diaphragm, from = 26, to = 34]
> ]]
> ]
>
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