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[bioontology-support] Annotator support email list submission

Trish Whetzel whetzel at stanford.edu
Thu Jul 22 18:13:59 PDT 2010


Hi Joey,

We received a new build of Mgrep that treats "_" the same as the  
alphabet, therefore the input text is not split on the underscore. We  
will test this tomorrow and work on getting this into production.

Trish


On Jul 12, 2010, at 10:27 AM, Joey Geiger wrote:

> I don't remember what the support email was for the annotator (I re- 
> installed my OS). I wanted to pass along something that I think is a  
> bit odd.
>
> When I try to parse the text "RatBrain_CTL_IBN_Rep1" it considers _  
> to be whitespace and breaks up the characters into chunks. Is there  
> a way to get it to consider text with underlines to be considered  
> complete words?
>
> Results from the HTML version of the site is below so you can get my  
> parameters. First is an actual request using the Cell Type. Next is  
> a made up example using the rat strain ontology. While the term "SD"  
> does appear in the text, since it's separated by "_" I would think  
> that it should be considered a whole word.
>
> Thanks.
>
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_671a
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(ISA_CLOSURE, 0) , (MAPPING, 2) , (MGREP, 0) ]
> 	parameters = [longestOnly = false, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = true, scored = true,  
> ontologiesToExpand = [], ontologiesToKeepInResult = [1006],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [a, about, above, across, after,  
> again, against, all, almost, alone, along, already, also, although,  
> always, among, an, and, another, any, anybody, anyone, anything,  
> anywhere, are, area, areas, around, as, ask, asked, asking, asks,  
> at, away, b, back, backed, backing, backs, be, became, because,  
> become, becomes, been, before, began, behind, being, beings, best,  
> better, between, big, both, but, by, c, came, can, cannot, case,  
> cases, certain, certainly, clear, clearly, come, could, d, did,  
> differ, different, differently, do, does, done, down, down, downed,  
> downing, downs, during, e, each, early, either, end, ended, ending,  
> ends, enough, even, evenly, ever, every, everybody, everyone,  
> everything, everywhere, f, face, faces, fact, facts, far, felt, few,  
> find, finds, first, for, four, from, full, fully, further,  
> furthered, furthering, furthers, g, gave, general, generally, get,  
> gets, give, given, gives, go, going, good, goods, got, great,  
> greater, greatest, group, grouped, grouping, groups, h, had, has,  
> have, having, he, her, here, herself, high, high, high, higher,  
> highest, him, himself, his, how, however, i, if, important, in,  
> interest, interested, interesting, interests, into, is, it, its,  
> itself, j, just, k, keep, keeps, kind, knew, know, known, knows, l,  
> large, largely, last, later, latest, least, less, let, lets, like,  
> likely, long, longer, longest, m, made, make, making, man, many,  
> may, me, member, members, men, might, more, most, mostly, mr, mrs,  
> much, must, my, myself, n, necessary, need, needed, needing, needs,  
> never, new, new, newer, newest, next, no, nobody, non, noone, not,  
> nothing, now, nowhere, number, numbers, o, of, off, often, old,  
> older, oldest, on, once, one, only, open, opened, opening, opens,  
> or, order, ordered, ordering, orders, other, others, our, out, over,  
> p, part, parted, parting, parts, per, perhaps, place, places, point,  
> pointed, pointing, points, possible, present, presented, presenting,  
> presents, problem, problems, put, puts, q, quite, r, rather, really,  
> right, right, room, rooms, s, said, same, saw, say, says, second,  
> seconds, see, seem, seemed, seeming, seems, sees, several, shall,  
> she, should, show, showed, showing, shows, side, sides, since,  
> small, smaller, smallest, so, some, somebody, someone, something,  
> somewhere, state, states, still, still, such, sure, t, take, taken,  
> than, that, the, their, them, then, there, therefore, these, they,  
> thing, things, think, thinks, this, those, though, thought,  
> thoughts, three, through, thus, to, today, together, too, took,  
> toward, turn, turned, turning, turns, two, u, under, until, up,  
> upon, us, use, used, uses, v, very, w, want, wanted, wanting, wants,  
> was, way, ways, we, well, wells, went, were, what, when, where,  
> whether, which, while, who, whole, whose, why, will, with, within,  
> without, work, worked, working, works, would, x, y, year, years,  
> yet, you, young, younger, youngest, your, yours, z, et],  
> withDefaultStopWords = false, isStopWordsCaseSenstive = false, text  
> to annotate = RatBrain_CTL_IBN_Rep1]
> ]
> 	ontologies = [[Cell type, nbAnnotation: 2, score: 14, (42768, 1.43,  
> 1006)]]
> 	annotations = [AnnotationBean [
> 		score = 7
> 		concept = [localConceptId: 42768/CL:0000794, conceptId: 7984493,  
> localOntologyId: 42768, isTopLevel: 0, fullId: http://purl.obolibrary.org/obo/CL_0000794 
> , preferredName: CD8-positive, alpha-beta cytotoxic T cell,  
> definitions: [], synonyms: [cytotoxic T-lymphocyte, CD8-positive,  
> alpha-beta cytotoxic T-lymphocyte, CD8-positive, alpha-beta  
> cytotoxic T-cell, cytotoxic T-cell, cytotoxic T cell, cytotoxic T  
> lymphocyte, CD8-positive, alpha-beta cytotoxic T lymphocyte],  
> semanticTypes: [[id: 10675850, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), from = 10, to = 12, mappedConcept =  
> [localConceptId: 42838/Cytotoxic_T-Lymphocyte, conceptId: 7913345,  
> localOntologyId: 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cytotoxic_T-Lymphocyte 
> , preferredName: Cytotoxic T-Lymphocyte, definitions: [], synonyms:  
> [Cell-Mediated Lympholytic Cells, Cytotoxic T Cell, T-Lymphocytes,  
> Cytotoxic, CTL, T-Lymphocyte, Cytotoxic, Cytotoxic T Cells,  
> Cytolytic T-Cell, Cytotoxic T-Lymphocytes], semanticTypes: [[id:  
> 10600838, semanticType: T025, description: Cell]]], mappingType =  
> Automatic, ]
> ], AnnotationBean [
> 		score = 7
> 		concept = [localConceptId: 42768/CL:0000910, conceptId: 7984607,  
> localOntologyId: 42768, isTopLevel: 0, fullId: http://purl.obolibrary.org/obo/CL_0000910 
> , preferredName: cytotoxic T cell, definitions: [], synonyms:  
> [cytotoxic T-lymphocyte, cytotoxic T-cell, cytotoxic T lymphocyte],  
> semanticTypes: [[id: 10675964, semanticType: T999, description: NCBO  
> BioPortal concept]]]
> 		context = [MAPPING(false), from = 10, to = 12, mappedConcept =  
> [localConceptId: 42838/Cytotoxic_T-Lymphocyte, conceptId: 7913345,  
> localOntologyId: 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cytotoxic_T-Lymphocyte 
> , preferredName: Cytotoxic T-Lymphocyte, definitions: [], synonyms:  
> [Cell-Mediated Lympholytic Cells, Cytotoxic T Cell, T-Lymphocytes,  
> Cytotoxic, CTL, T-Lymphocyte, Cytotoxic, Cytotoxic T Cells,  
> Cytolytic T-Cell, Cytotoxic T-Lymphocytes], semanticTypes: [[id:  
> 10600838, semanticType: T025, description: Cell]]], mappingType =  
> Automatic, ]
> ]]
> ]
>
>
> ObaResultBean [
> ResultBean [
> 	resultID = OBA_RESULT_7fa3
> 	dictionary = [id = 3, name = OBS_DICO_7281, dateCreated =  
> 2009-06-17 16:19:47.0]
> 	statistics = [(MAPPING, 2) , (MGREP, 1) , (ISA_CLOSURE, 0) ]
> 	parameters = [longestOnly = false, wholeWordOnly = true,  
> filterNumber = true, withSynonyms = true, scored = true,  
> ontologiesToExpand = [], ontologiesToKeepInResult = [1150],  
> isVirtualOntologyId = true, semanticTypes = [], levelMax = 0,  
> mappingTypes = [], stopWords = [a, about, above, across, after,  
> again, against, all, almost, alone, along, already, also, although,  
> always, among, an, and, another, any, anybody, anyone, anything,  
> anywhere, are, area, areas, around, as, ask, asked, asking, asks,  
> at, away, b, back, backed, backing, backs, be, became, because,  
> become, becomes, been, before, began, behind, being, beings, best,  
> better, between, big, both, but, by, c, came, can, cannot, case,  
> cases, certain, certainly, clear, clearly, come, could, d, did,  
> differ, different, differently, do, does, done, down, down, downed,  
> downing, downs, during, e, each, early, either, end, ended, ending,  
> ends, enough, even, evenly, ever, every, everybody, everyone,  
> everything, everywhere, f, face, faces, fact, facts, far, felt, few,  
> find, finds, first, for, four, from, full, fully, further,  
> furthered, furthering, furthers, g, gave, general, generally, get,  
> gets, give, given, gives, go, going, good, goods, got, great,  
> greater, greatest, group, grouped, grouping, groups, h, had, has,  
> have, having, he, her, here, herself, high, high, high, higher,  
> highest, him, himself, his, how, however, i, if, important, in,  
> interest, interested, interesting, interests, into, is, it, its,  
> itself, j, just, k, keep, keeps, kind, knew, know, known, knows, l,  
> large, largely, last, later, latest, least, less, let, lets, like,  
> likely, long, longer, longest, m, made, make, making, man, many,  
> may, me, member, members, men, might, more, most, mostly, mr, mrs,  
> much, must, my, myself, n, necessary, need, needed, needing, needs,  
> never, new, new, newer, newest, next, no, nobody, non, noone, not,  
> nothing, now, nowhere, number, numbers, o, of, off, often, old,  
> older, oldest, on, once, one, only, open, opened, opening, opens,  
> or, order, ordered, ordering, orders, other, others, our, out, over,  
> p, part, parted, parting, parts, per, perhaps, place, places, point,  
> pointed, pointing, points, possible, present, presented, presenting,  
> presents, problem, problems, put, puts, q, quite, r, rather, really,  
> right, right, room, rooms, s, said, same, saw, say, says, second,  
> seconds, see, seem, seemed, seeming, seems, sees, several, shall,  
> she, should, show, showed, showing, shows, side, sides, since,  
> small, smaller, smallest, so, some, somebody, someone, something,  
> somewhere, state, states, still, still, such, sure, t, take, taken,  
> than, that, the, their, them, then, there, therefore, these, they,  
> thing, things, think, thinks, this, those, though, thought,  
> thoughts, three, through, thus, to, today, together, too, took,  
> toward, turn, turned, turning, turns, two, u, under, until, up,  
> upon, us, use, used, uses, v, very, w, want, wanted, wanting, wants,  
> was, way, ways, we, well, wells, went, were, what, when, where,  
> whether, which, while, who, whole, whose, why, will, with, within,  
> without, work, worked, working, works, would, x, y, year, years,  
> yet, you, young, younger, youngest, your, yours, z, et],  
> withDefaultStopWords = false, isStopWordsCaseSenstive = false, text  
> to annotate = CHEESE_SD_BURGER]
> ]
> 	ontologies = [[Rat Strain Ontology, nbAnnotation: 3, score: 24,  
> (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 = 8, to = 9, [name: SD,  
> localConceptId: 42515/RS:0000681, isPreferred: true, dictionaryId:  
> 3], ]
> ], AnnotationBean [
> 		score = 7
> 		concept = [localConceptId: 42515/RS:0001409, conceptId: 4622434,  
> localOntologyId: 42515, isTopLevel: 0, fullId: RS:0001409,  
> preferredName: N:SD, definitions: [], synonyms: [SDN:SD, SD/N, RRRC: 
> 0239, Sprague-Dawley , Sprague Dawley ], semanticTypes: [[id:  
> 7218481, semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), from = 8, to = 9, mappedConcept =  
> [localConceptId: 42838/Sudan, conceptId: 7960454, localOntologyId:  
> 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Sudan 
> , preferredName: Sudan, definitions: [], synonyms: [SU, SDN, 736,  
> SD], semanticTypes: [[id: 10650950, semanticType: T083, description:  
> Geographic Area]]], mappingType = Automatic, ]
> ], AnnotationBean [
> 		score = 7
> 		concept = [localConceptId: 42515/RS:0000706, conceptId: 4621733,  
> localOntologyId: 42515, isTopLevel: 0, fullId: RS:0000706,  
> preferredName: SDT.ZDF-Leprfa/Jtt, definitions: [], synonyms: [RGD  
> ID: 2314027, SDT.Cg-Leprfa/Jtp, SDT fatty], semanticTypes: [[id:  
> 7217780, semanticType: T999, description: NCBO BioPortal concept]]]
> 		context = [MAPPING(false), from = 8, to = 9, mappedConcept =  
> [localConceptId: 42838/Sudan, conceptId: 7960454, localOntologyId:  
> 42838, isTopLevel: 0, fullId: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Sudan 
> , preferredName: Sudan, definitions: [], synonyms: [SU, SDN, 736,  
> SD], semanticTypes: [[id: 10650950, semanticType: T083, description:  
> Geographic Area]]], mappingType = Automatic, ]
> ]]
> ]
>
>




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