Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Annotator: Issue with from/to values in MGREP

Joey Geiger jfgeiger at mcw.edu
Mon Mar 22 14:23:01 PDT 2010


http://rest.bioontology.org/test_oba.html

All parameters default except:

ontologiesToKeepInResult: 1000
isVirtualOntologyId: true
textToAnnotate: Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils. The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation. The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood. After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer. Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube. The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX). The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 5 day time point
format: text


results:

], AnnotationBean [ 
		score = 32
		concept = [localConceptId: 42311/MA:0001693, conceptId: 3272272, localOntologyId: 42311, isTopLevel: 1, preferredName: urinary bladder urothelium, synonyms: [transitional epithelium], semanticTypes: [[id: 5131684, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MGREP(true), [name: transitional epithelium, localConceptId: 42311/MA:0001693, isPreferred: false, dictionaryId: 3], from = 1011, to = 1033]

In a text editor characters 1011-1033 of the text above are:  ansitional epithelium w

I believe this is an issue with the ° (degree) symbols being counted as 2 characters instead of one. While the ° is a double byte character it only takes up one column as printed text which seems to throw off display based on the from-to.

Quick test:

ontologiesToKeepInResult: 1000
isVirtualOntologyId: true
textToAnnotate: °°transitional epithelium

results:

], AnnotationBean [ 
		score = 32
		concept = [localConceptId: 42311/MA:0001693, conceptId: 3272272, localOntologyId: 42311, isTopLevel: 1, preferredName: urinary bladder urothelium, synonyms: [transitional epithelium], semanticTypes: [[id: 5131684, semanticType: T999, description: NCBO BioPortal concept]]]
		context = [MGREP(true), [name: transitional epithelium, localConceptId: 42311/MA:0001693, isPreferred: false, dictionaryId: 3], from = 5, to = 27]




More information about the bioontology-support mailing list