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

Joey Geiger jfgeiger at mcw.edu
Wed Jul 21 11:31:44 PDT 2010


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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