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[bioontology-support] annotator 'longest only' parameter loses annotations

Joey Geiger jfgeiger at mcw.edu
Tue Apr 19 11:15:41 PDT 2011


I'm trying to figure out why the 'longest only' parameter set to true is removing results.

With longest only off, I get 2 mapped results for muscle and get separate 'stomach' and 'stomach wall' annotations. (Some MAPPINGS were removed to shorten the results for inclusion)

ObaResultBean [ 
ResultBean [ 
	resultID = OBA_RESULT_a998
	statistics = [(MAPPING, 16) , (CLOSURE, 0) , (MGREP, 2) ]
	parameters = [longestOnly = false, wholeWordOnly = true, filterNumber = true, withSynonyms = true, withContext = true, ontologiesToExpand = [], ontologiesToKeepInResult = [1000], isVirtualOntologyId = true, semanticTypes = [], levelMax = 0, mappingTypes = [], stopWords = [], withDefaultStopWords = false, isStopWordsCaseSenstive = false, text to annotate = skeletal muscle stomach wall]
]
	ontologies = [[Mouse adult gross anatomy, nbAnnotation: 18, score: 1658, (45065, 1.207, 1000)]]
	annotations = [AnnotationBean [ 
		score = 108
		concept = [localConceptId: 45065/MA:0000353, conceptId: 16754492, localOntologyId: 45065, isTopLevel: 0, fullId: http://purl.org/obo/owl/MA#MA_0000353, preferredName: stomach, definitions: [], synonyms: [], semanticTypes: [[id: 20261123, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MAPPING(false), from = 17, to = 23, mappedConcept = [localConceptId: 45040/EHDA:5799, conceptId: 16938785, localOntologyId: 45040, isTopLevel: 0, fullId: http://purl.org/obo/owl/EHDA#EHDA_5799, preferredName: stomach, definitions: [], synonyms: [], semanticTypes: [[id: 20445416, semanticType: T999, description: NCBO BioPortal concept]]], mappingType = Automatic, ]
], AnnotationBean [ 
		score = 108
		concept = [localConceptId: 45065/MA:0000353, conceptId: 16754492, localOntologyId: 45065, isTopLevel: 0, fullId: http://purl.org/obo/owl/MA#MA_0000353, preferredName: stomach, definitions: [], synonyms: [], semanticTypes: [[id: 20261123, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MGREP(true), from = 17, to = 23, [name: stomach, localConceptId: 45065/MA:0000353, isPreferred: true], ]
], AnnotationBean [ 
		score = 14
		concept = [localConceptId: 45065/MA:0000015, conceptId: 16754156, localOntologyId: 45065, isTopLevel: 0, fullId: http://purl.org/obo/owl/MA#MA_0000015, preferredName: muscle organ, definitions: [], synonyms: [], semanticTypes: [[id: 20260787, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MAPPING(false), from = 10, to = 15, mappedConcept = [localConceptId: 42838/Muscle, conceptId: 15665055, localOntologyId: 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Muscle, preferredName: Muscle, definitions: [], synonyms: [Muscular], semanticTypes: [[id: 19137421, semanticType: T999, description: NCBO BioPortal concept]]], mappingType = Manual, ]
], AnnotationBean [ 
		score = 14
		concept = [localConceptId: 45065/MA:0000015, conceptId: 16754156, localOntologyId: 45065, isTopLevel: 0, fullId: http://purl.org/obo/owl/MA#MA_0000015, preferredName: muscle organ, definitions: [], synonyms: [], semanticTypes: [[id: 20260787, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MAPPING(false), from = 10, to = 15, mappedConcept = [localConceptId: 45061/ZFA:0005145, conceptId: 16881603, localOntologyId: 45061, isTopLevel: 0, fullId: http://purl.org/obo/owl/ZFA#ZFA_0005145, preferredName: muscle, definitions: [], synonyms: [muscles], semanticTypes: [[id: 20388234, semanticType: T999, description: NCBO BioPortal concept]]], mappingType = Automatic, ]
], AnnotationBean [ 
		score = 10
		concept = [localConceptId: 45065/MA:0002692, conceptId: 16756809, localOntologyId: 45065, isTopLevel: 0, fullId: http://purl.org/obo/owl/MA#MA_0002692, preferredName: stomach wall, definitions: [], synonyms: [], semanticTypes: [[id: 20263440, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MGREP(true), from = 17, to = 28, [name: stomach wall, localConceptId: 45065/MA:0002692, isPreferred: true], ]
]]
]

When I set 'longest only' to true, I get no results for muscle and only a single (proper) result for 'stomach wall'.

ObaResultBean [ 
ResultBean [ 
	resultID = OBA_RESULT_a9e7
	statistics = [(MAPPING, 0) , (CLOSURE, 0) , (MGREP, 1) ]
	parameters = [longestOnly = true, wholeWordOnly = true, filterNumber = true, withSynonyms = true, withContext = true, ontologiesToExpand = [], ontologiesToKeepInResult = [1000], isVirtualOntologyId = true, semanticTypes = [], levelMax = 0, mappingTypes = [], stopWords = [], withDefaultStopWords = false, isStopWordsCaseSenstive = false, text to annotate = skeletal muscle stomach wall]
]
	ontologies = [[Mouse adult gross anatomy, nbAnnotation: 1, score: 10, (45065, 1.207, 1000)]]
	annotations = [AnnotationBean [ 
		score = 10
		concept = [localConceptId: 45065/MA:0002692, conceptId: 16756809, localOntologyId: 45065, isTopLevel: 0, fullId: http://purl.org/obo/owl/MA#MA_0002692, preferredName: stomach wall, definitions: [], synonyms: [], semanticTypes: [[id: 20263440, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MGREP(true), from = 17, to = 28, [name: stomach wall, localConceptId: 45065/MA:0002692, isPreferred: true], ]
]]
]

Isn't the idea that it should match something no matter what, and if there's something 'longer' it should use that result? I know this probably has something to do with the mapping functionality, but from a use standpoint it's rather annoying. I have to keep it off all the time since it will miss annotations that clearly exist, but at the same time gives me multiple sub-annotations for a clearly more specific term.

Thanks.


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