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

Trish Whetzel whetzel at stanford.edu
Tue Apr 27 12:19:48 PDT 2010


Hi Joey,

Both problems that you reported are now fixed. The error with seeing  
two different sets of results was due to an error in the configuration  
of one of the instances of MGREP. The process that led to this has  
been changed and should not occur in the future.

The other issue related to the slowness of the web service occurred  
because 1 of the 3 servers the Annotator uses went down and was not  
automatically added back to the round-robin. We are looking into other  
ways to monitor this so that if a server experiences problems it will  
auto re-start.

Trish


On Apr 27, 2010, at 11:19 AM, Trish Whetzel wrote:

> 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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>
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