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[bioontology-support] Annotator not returning the correct start and end values with certain characters in text

Trish Whetzel whetzel at stanford.edu
Wed Jul 21 12:35:26 PDT 2010


Hi Joey,

Thanks for alerting us to this issue. I recall that a similar issue  
occurred in the past, but thought that it was fixed. Is this a re- 
occurrence of the same issue?

Trish


On Jul 21, 2010, at 11:31 AM, Joey Geiger wrote:

> If the text to annotate include some different characters
> ·
> ½
> º
> the start and end values returned are invalid. This issue is  
> compounded when there are multiple instances of those character types.
>
> Examples using http://rest.bioontology.org/test_oba.html
>
> Each example searches for the SD rat strain in the text.
>
> First is correctly identified as 1-2
> Second fails as 3-4 (should be 2-3) with · as first char
> Third fails as 3-4 (should be 2-3) with ½ as first char
> Fourth fails as 3-4 (should be 2-3) with º as first char
> Fifth fails as 7-8 (should be 4-5) with ·½º as first 3 characters
>
> Thank you.
>
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_0460
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(ISA_CLOSURE, 0) , (MGREP, 1) , (MAPPING, 0) ]
> 	parameters = [longestOnly = false, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = false, scored = true,  
> ontologiesToExpand = [1150], ontologiesToKeepInResult = [1150],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [], withDefaultStopWords = false,  
> isStopWordsCaseSenstive = false, text to annotate = SD]
> ]
> 	ontologies = [[Rat Strain Ontology, nbAnnotation: 1, score: 10,  
> (42515, 1.0, 1150)]]
> 	annotations = [AnnotationBean [
> 		score = 10
> 		concept = [localConceptId: 42515/RS:0000681, conceptId: 4621708,  
> localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000681,  
> preferredName: SD, definitions: [], synonyms: [Sprague-Dawley,  
> Sprague Dawley , RGD ID: 70508], semanticTypes: [[id: 7217755,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MGREP(true), from = 1, to = 2, [name: SD,  
> localConceptId: 42515/RS:0000681, isPreferred: true, dictionaryId:  
> 3], ]
> ]]
> ]
>
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_072d
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(MAPPING, 0) , (ISA_CLOSURE, 0) , (MGREP, 1) ]
> 	parameters = [longestOnly = false, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = false, scored = true,  
> ontologiesToExpand = [1150], ontologiesToKeepInResult = [1150],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [], withDefaultStopWords = false,  
> isStopWordsCaseSenstive = false, text to annotate = ·SD]
> ]
> 	ontologies = [[Rat Strain Ontology, nbAnnotation: 1, score: 10,  
> (42515, 1.0, 1150)]]
> 	annotations = [AnnotationBean [
> 		score = 10
> 		concept = [localConceptId: 42515/RS:0000681, conceptId: 4621708,  
> localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000681,  
> preferredName: SD, definitions: [], synonyms: [Sprague Dawley ,  
> Sprague-Dawley, RGD ID: 70508], semanticTypes: [[id: 7217755,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MGREP(true), from = 3, to = 4, [name: SD,  
> localConceptId: 42515/RS:0000681, isPreferred: true, dictionaryId:  
> 3], ]
> ]]
> ]
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_7519
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(MAPPING, 0) , (ISA_CLOSURE, 0) , (MGREP, 1) ]
> 	parameters = [longestOnly = false, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = false, scored = true,  
> ontologiesToExpand = [1150], ontologiesToKeepInResult = [1150],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [], withDefaultStopWords = false,  
> isStopWordsCaseSenstive = false, text to annotate = ½SD]
> ]
> 	ontologies = [[Rat Strain Ontology, nbAnnotation: 1, score: 10,  
> (42515, 1.0, 1150)]]
> 	annotations = [AnnotationBean [
> 		score = 10
> 		concept = [localConceptId: 42515/RS:0000681, conceptId: 4621708,  
> localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000681,  
> preferredName: SD, definitions: [], synonyms: [Sprague Dawley ,  
> Sprague-Dawley, RGD ID: 70508], semanticTypes: [[id: 7217755,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MGREP(true), from = 3, to = 4, [name: SD,  
> localConceptId: 42515/RS:0000681, isPreferred: true, dictionaryId:  
> 3], ]
> ]]
> ]
>
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_4e9d
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(MGREP, 1) , (MAPPING, 0) , (ISA_CLOSURE, 0) ]
> 	parameters = [longestOnly = false, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = false, scored = true,  
> ontologiesToExpand = [1150], ontologiesToKeepInResult = [1150],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [], withDefaultStopWords = false,  
> isStopWordsCaseSenstive = false, text to annotate = ºSD]
> ]
> 	ontologies = [[Rat Strain Ontology, nbAnnotation: 1, score: 10,  
> (42515, 1.0, 1150)]]
> 	annotations = [AnnotationBean [
> 		score = 10
> 		concept = [localConceptId: 42515/RS:0000681, conceptId: 4621708,  
> localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000681,  
> preferredName: SD, definitions: [], synonyms: [RGD ID: 70508,  
> Sprague Dawley , Sprague-Dawley], semanticTypes: [[id: 7217755,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MGREP(true), from = 3, to = 4, [name: SD,  
> localConceptId: 42515/RS:0000681, isPreferred: true, dictionaryId:  
> 3], ]
> ]]
> ]
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_9450
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(MGREP, 1) , (MAPPING, 0) , (ISA_CLOSURE, 0) ]
> 	parameters = [longestOnly = false, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = false, scored = true,  
> ontologiesToExpand = [1150], ontologiesToKeepInResult = [1150],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [], withDefaultStopWords = false,  
> isStopWordsCaseSenstive = false, text to annotate = ·½ºSD]
> ]
> 	ontologies = [[Rat Strain Ontology, nbAnnotation: 1, score: 10,  
> (42515, 1.0, 1150)]]
> 	annotations = [AnnotationBean [
> 		score = 10
> 		concept = [localConceptId: 42515/RS:0000681, conceptId: 4621708,  
> localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000681,  
> preferredName: SD, definitions: [], synonyms: [Sprague Dawley ,  
> Sprague-Dawley, RGD ID: 70508], semanticTypes: [[id: 7217755,  
> semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MGREP(true), from = 7, to = 8, [name: SD,  
> localConceptId: 42515/RS:0000681, isPreferred: true, dictionaryId:  
> 3], ]
> ]]
> ]
>
>
>

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